News archive

Discord channel for GPUGRID
Hi,
I have created a discord channel for GPUGRID. It kind of duplicates this in some aspects but maybe people are more used to Discord.

It is an additional channel that may help to build up the community.

JOIN:
https://discord.gg/abpWXawZ7v

GDF 13 Feb 2024 | 11:29:01 UTC · Comment

PYSCFbeta: Quantum chemistry calculations on GPU
Hello GPUGRID!

We are deploying a new app "PYSCFbeta: Quantum chemistry calculations on GPU". It is currently in testing/beta stage. It is only on Linux at the moment.

The app performs quantum chemistry calculations. At the moment we are using it specifically for Density Functional Theory calculations: http://en.wikipedia.org/wiki/Density_functional_theory

These types of calculations allow us to accurately compute specific properties of small molecules.

The current test work units have a runtime of the order 1hr (very much dependent on the GPU speed and size of molecule). Each work unit currently contains 1 molecule with ~10 configurations.

The app will not work on GPUs with compute capability less than 6.0. It should not be sending them to these cards but I think at the moment this functionality is not working properly.

The work-units require a lot of GPU memory. It works best if the work-unit is the only thing running on the GPU. If other programs are using significant GPU memory the work-unit might fail.

Looking forward to hearing feedback from you.

Steve 12 Jan 2024 | 13:03:21 UTC · Comment

ATM
Hello GPUGRID!

You‘ve already noticed that a new app called “ATM” has been deployed with some test runs. We are working on its validation and deployment, so expect more jobs to come on this app soon. Let me briefly explain what this new app is about.

The ATM application

The new ATM application stands for Alchemical Transfer Method, a methodology Emilio Gallicchio et al. designed for absolute and relative binding affinity predictions. The ATM method allows us to estimate binding affinities for molecules against a specific protein, measuring the strength at which they bind. This methodology falls under the category of alchemical free energy calculation methods, where unphysical intermediate states are used to estimate the free energy of physical processes (such as protein-ligand binding). The benefits of ATM, when compared with other common free energy prediction methods (like the popular FEP), come from its simplicity, as it can be used with any forcefield and does not require a lot of expertise to make it work properly.

Measuring experimental binding affinities between candidate molecules and the targeted protein is one of the first steps in drug discovery projects, but synthesizing molecules and performing experiments is expensive. Having the capacity to perform computational binding affinity predictions, particularly during drug lead optimization, is extremely beneficial. We are actively working now on testing and validating the ATM method so that we can start applying it to real drug discovery projects as soon as possible. Additionally, since these methods are usually applied to hundreds of molecules, it benefits a lot from the parallelization capabilities of GPUGRID, so if everything goes as expected, this could potentially send lots of work units.

The ATM app is based on Python, similar to the PythonRL application, where we ship it with a specific python environment.

Here are the two main references for the ATM method, for both absolute and relative binding affinity predictions:

Absolute binding free energy estimation with ATM: https://arxiv.org/pdf/2101.07894.pdf
Relative binding free energy estimation with ATM:
https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129

For now we are only able to send jobs to Linux machines but we are hoping to have a Windows version soon.

3 Mar 2023 | 10:39:46 UTC · Comment

ACEMD updated app
As I said. We are currently compiling the Windows version.

GDF 10 Jan 2023 | 9:53:01 UTC · Comment

ACEMD 4
Hello everybody,

You probably have noticed the new ACEMD 4 app and have a few questions.

What is the difference between ACEMD 3 and ACEMD 4?

What is NNP/MM?

https://arxiv.org/abs/2201.08110

How much more accurate is NNP?

https://arxiv.org/abs/2202.02541

What are software/hardware requirements for ACEMD 4?

https://pytorch.org

When will ACEMD 3 be replaced by ACEMD 4?

What will happen next?

Happy computing,

Raimondas 1 Mar 2022 | 12:37:14 UTC · Comment

Dlls under windows
Is this still a problem?

"
There is still the issue with the bundled zip files not containing the Visual C++ redistributable runtime vcruntime140_1.dll for Windows hosts.
"

GDF 1 Dec 2021 | 18:12:18 UTC · Comment

Change in the scheduler
I have made a change in the scheduler code yesterday. Let me know if now the server is assigning the correct application:
Cuda10.1 for old drivers
Cuda11 for newer drivers

GDF 1 Dec 2021 | 15:21:51 UTC · Comment

Issue with certificates
Somehow the program to update the certificates stopped working. Now it is ok and the project is fine again. 29 Nov 2021 | 16:32:16 UTC · Comment

Job offer for PhD and Postdoctoral positions
We have two openings for a PhD and a postdoc. If you know anybody that could be interested, share it please.

https://www.compscience.org

GDF 26 Oct 2021 | 17:38:33 UTC · Comment

Python Runtime (GPU, beta)
If anybody wants to help debug a new application, please enable the above mentioned app. 26 Oct 2021 | 10:57:36 UTC · Comment

What is happening and what will happen at GPUGRID, update for 2021
As you know, GPUGRID was the first BOINC project to run GPU applications, in fact we help in creating the infrastructure for that. This was very many years ago and since then many things changed. In particular, recently, we had not a constant stream of workunits. I would like to explain the present and expected future of GPUGRID here.

In the last few years, we moved from doing science by running very many simulations to develop new methods at the boundary between physical simulations and machine learning methods/artificial intelligence. These new methods did not require a lot of simulations and most of the PhD students in the research group did not use GPUGRID daily. We still had some long term project running on GPUGRID for which you will see results shortly in terms of new scientific publications.

Among other things ACEMD, the application behind GPUGRID is now built partially using OpenMM, of which I am also principal investigator. As you might know OpenMM is also used in Folding@Home. We have received a grant to develop OpenMM very recently with one or two people starting before the end of the year. This will be good for GPUGRID because it means that we will be using GPUGRID a lot more.

Furthermore, we recently found a way to run AI simulations in GPUGRID. We have only run very few test cases, but there is a PhD student in the lab with a thesis on cooperative intelligence, where very many AI agents collaborate to solve tasks. The goal is to understand how cooperative intelligence works. We are also looking for a postdoc in cooperative intelligence, in case you know somebody.

https://www.compscience.org

I hope that this clarify the current situation. On the practical term, we expect to have the ACEMD application fixed for RTX30xx within few weeks, as now the developper of ACEMD is also doing the deployment on GPUGRID, making everything simpler.

GDF 7 Aug 2021 | 6:44:06 UTC · Comment

Server problems
We are experiencing multiple issues, e.g. hitting an undocumented upload size limit, and others. Please be patient. 5 Jul 2021 | 9:00:34 UTC · Comment

Update acemd3 app
I deployed the new app, which now requires cuda 11.2 and hopefully support all the latest cards. Touching the cuda versions is always a nightmare in boinc scheduler so expect problems.

1 Jul 2021 | 18:29:57 UTC · Comment

Experimental Python tasks (beta) - task description
Hello everyone, just wanted to give some updates about the machine learning - python jobs that Toni mentioned earlier in the "Experimental Python tasks (beta) " thread.

What are we trying to accomplish?
We are trying to train populations of intelligent agents in a distributed computational setting to solve reinforcement learning problems. This idea is inspired in the fact that human societies are knowledgeable as a whole, while individual agents have limited information. Also, every new generation of individuals attempts to expand and refine the knowledge inherited from previous ones, and the most interesting discoveries become part of a corpus of common knowledge. The idea is that small groups of agents will train in GPUgrid machines, and report their discoveries and findings. Information of multiple agents can be put in common and conveyed to new generations of machine learning agents. To the best of our knowledge this is the first time something of this sort is attempted in a GPUGrid-like platform, and has the potential to scale to solve problems unattainable in smaller scale settings.

Why most jobs were failing a few weeks ago?
It took us some time and testing to make simple agents work, but we managed to solve the problems in the previous weeks. Now, almost all agents train successfully.

Why are GPUs being underutilized? and why are CPU used for?
In the previous weeks we were running small scale tests, with small neural networks models that occupied little GPU memory. Also, some reinforcement learning environments, especially simple ones like those used in the test, run on CPU. Our idea is to scale to more complex models and environments to exploit the GPU capacity of the grid.

More information:
We use mainly PyTorch to train our neural networks. We only use Tensorboard because it is convenient for logging. We might remove that dependency in the future. 17 Jun 2021 | 10:40:32 UTC · Comment

New D3RBanditTest workunits
Dears,

as you may have noticed, we sent a new batch of WUs for a new experiment. This time the WUs are rather large and require relatively new cards. For reference, should be ~18h on a 1080 Ti.

Thanks!

T 15 Feb 2021 | 9:09:13 UTC · Comment

Happy new year!
Dear all,

we at Gpugrid would like to wish you a merry ending of 2020 and wish the best for the coming new year!

Thanks for your continued support.

T 31 Dec 2020 | 16:43:14 UTC · Comment

Project restarted
Sorry for the downtime. 21 Dec 2020 | 13:53:44 UTC · Comment

Disk full - solved
We have a situation, and no quick solution. I'm suspending the project. 19 Dec 2020 | 13:47:01 UTC · Comment

New donation system
We have updated the donation system provided by the university. It should work now and should be simpler than what was available before.

If you want to donate go ahead at http://www.gpugrid.net/gpugrid_donations.php

Put your userid or username in the name field so that we know and we can add the donor badge.

gdf 25 Nov 2020 | 22:49:39 UTC · Comment

Experimental Python tasks (beta)
I'm creating some experimental tasks for the Python app (made Beta). They are Linux and CUDA specific and serve in preparation for future batches.

They may use a relatively large amount of disk space (order of 1-10 GB) which persists between runs, and is cleared if you reset the project.

13 Oct 2020 | 6:07:19 UTC · Comment

Project restarted
Dears, thanks for your patience.

I updated the acemd3 apps.

Also, I verified that there were very few results by apps from the old CUDA version, so I won't be re-deploying them. In other words, apps now require CUDA 10 (Linux) and CUDA 10.1 (Windows). In terms of drivers versions:

CUDA 10.1 (10.1.105) >= 418.39 for Windows
CUDA 10.0 (10.0.130) >= 410.48 for Linux

https://docs.nvidia.com/deploy/cuda-compatibility/index.html 9 Oct 2020 | 13:20:48 UTC · Comment

Suspending project
Until we update the app. Sorry. 7 Oct 2020 | 17:51:31 UTC · Comment

New paper: Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations.
Another great GPUGRID-based work: studying the possible modulation of intrinsically disordered proteins through drugs.

Herrera-Nieto P, Pérez A, De Fabritiis G, Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of chemical information and modeling 2020. doi:10.1021/acs.jcim.0c00381

The corresponding badge is labeled "Herrera-Nieto, JCIM 2020".

The extreme dynamic behavior of intrinsically disordered proteins hinders the development of drug-like compounds capable of modulating them. There are several examples of small molecules that specifically interact with disordered peptides. However, their mechanisms of action are still not well understood. Here, we use extensive molecular dynamics simulations combined with adaptive sampling algorithms to perform free ligand binding studies in the context of intrinsically disordered proteins. We tested this approach in the system composed by the D2 sub-domain of the disordered protein p27 and the small molecule SJ403. The results show several protein–ligand bound states characterized by the establishment of a loosely oriented interaction mediated by a limited number of contacts between the ligand and critical residues of p27. Finally, protein conformations in the bound state are likely to be explored by the isolated protein too, therefore supporting a model where the addition of the small molecule restricts the available conformational space.

9 Sep 2020 | 9:24:39 UTC · Comment

New paper: Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting…

Here we studied a possible mode of action of NF023, a molecule which disrupts some protein-protein interactions (cIAP-TRAF) misregulated in cancer. The molecule is very charged and flexible, so classical docking studies aren't up to a full modeling... but large-scale MD powered by GPUGRID is.

Cossu F, Sorrentino L, Fagnani E, Zaffaroni M, Milani M, Giorgino T, Mastrangelo E. Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly. J Chem Inf Model. 2020 Aug 21 doi:10.1021/acs.jcim.0c00518

Protein-protein interactions are the basis of many important physiological processes, and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitors of apoptosis (IAPs)-mediated interactions are pivotal for cancer cell survival; the interaction of the BIR1 domain of cIAP2 with TRAF2 was shown to lead the recruitment of cIAPs to the TNF-receptor, promoting the activation of NF-κB survival pathway. In this work, using a combined in silico-in vitro approach we identified a drug-like molecule, NF023, able to disrupt cIAP2 interaction with TRAF2. We demonstrated in vitro its ability to interfere with the assembly of the cIAP2-BIR1/TRAF2 complex and performed a thorough characterization of the compound’s mode of action through 248 parallel unbiased molecular dynamics simulations of 300 ns (totaling almost 75 µs of all-atom sampling), which identified multiple binding modes to the BIR1 domain of cIAP2 via clustering and ensemble docking. NF023 is, thus, a promising protein-protein interaction disruptor, representing a starting point to develop modulators of NF-κB-mediated cell survival in cancer. This study represents a model-procedure that shows the use of large-scale molecular dynamics methods to typify promiscuous interactors.

2 Sep 2020 | 8:05:21 UTC · Comment

Science pages updated
Should now reflect the list of papers and badges.
Some data, e.g. images, is missing. 31 Aug 2020 | 9:17:38 UTC · Comment

New paper: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations
The latest scientific publication obtained with your support and computation is here:

Herrera-Nieto, P., Pérez, A. & De Fabritiis, G. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Sci Rep 10, 12402 (2020).

It investigates an open and difficult problem in biology, namely the structure-function relationship of intrinsically disordered proteins (IDP). IDP proteins are involved in many regulatory processes, and yet are difficult to study both experimentally and computationally. The amount of power provided by GPUGRID volunteers came to the rescue, enabling very extensive sampling of p53, an exemplary IDP involved in oncogenic processes.

The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for ∼ 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel 𝛽-sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

26 Aug 2020 | 11:11:54 UTC · Comment

New paper 2/2: GPCRmd uncovers the dynamics of the 3D-GPCRome
The second paper is

Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S. et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods (2020). 10.1038/s41592-020-0884-y

here, your computations have been used to build a database of configurations for most types and subtypes of GPCR-class proteins. GPCRs are "do-all" receptors - there are many many subtypes, each with activators and inhibitors. The GPCRmd database provides for the first time a *systematic* coverage of their dynamics.

G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.

...

14310 1 107681600
101936 2 96720000
483287 3 83904600
500240 4 74393800
306281 5 57790200
93201 6 55775200
100499 7 53115400
504924 8 51664600
25378 9 50858600
62100 10 32240000
125700 11 31837000
73475 12 29983200
69336 13 27645800
28899 14 23615800
31053 15 22406800
146761 16 21439600
497873 17 20230600
13127 18 20069400
36684 19 19666400
126468 20 19021600

24 Jul 2020 | 16:26:51 UTC · Comment

New paper 1/2: PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulation
Two recent papers which came out with results from GPUGRID.

First,

PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations
Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, and Gianni De Fabritiis
Journal of Chemical Information and Modeling 2020 60 (4), 2314-2324
DOI: 10.1021/acs.jcim.9b01209

In this paper (and the corresponding live system) GPUGRID's computations are used to power a search for elusive (transient) pockets which may become drug targets.

Thanks for the contributions!

Cryptic pockets are protein cavities that remain hidden in resolved apo structures and generally require the presence of a co-crystallized ligand to become visible. Finding new cryptic pockets is crucial for structure-based drug discovery to identify new ways of modulating protein activity and thus expand the druggable space. We present here a new method and associated web application leveraging mixed-solvent molecular dynamics (MD) simulations using benzene as a hydrophobic probe to detect cryptic pockets. Our all-atom MD-based workflow was systematically tested on 18 different systems and 5 additional kinases and represents the largest validation study of this kind. CrypticScout identifies benzene probe binding hotspots on a protein surface by mapping probe occupancy, residence time, and the benzene occupancy reweighed by the residence time. The method is presented to the scientific community in a web application available via www.playmolecule.org using a distributed computing infrastructure to perform the simulations.

List of most-contributing users:

User Rank Credits
101936 1 4639746
14310 2 4450949
483287 3 3535477
103037 4 2362054
500240 5 1986559
25378 6 1969784
504924 7 1945416
100499 8 1834758
73475 9 1796967
125700 10 1755579
126468 11 1651313
306281 12 1638950
62100 13 1542475
21233 14 1536750
535400 15 1364758
13127 16 1161000
509733 17 1035000
28899 18 973950
543022 19 971404
89682 20 946350

24 Jul 2020 | 16:23:08 UTC · Comment

More tasks: MDAD*
I'm filling up the task queue again- - these are called MDAD and suffix.
Happy crunching!

T 21 May 2020 | 12:47:33 UTC · Comment

HTTPS
Now that the server is unloaded I'm trying to complete the switch to https. Please check if WUs up/download as usual (although I know that there are very few WUs). 20 May 2020 | 6:53:51 UTC · Comment

Summary of the MDAD effort
So, the huge MDAD batch that we sent at the end of January just finished crunching. That was by far the largest continuous load we placed on Gpugrid, so thanks everybody!

I will be sending more continuation workunits, but it will take some time to arrange the details. For the time being, take it as a deserved break :)

The objective of the batch was a large-scale exploration of the protein landscape. Its accumulated 25 ms of sampling will be useful for biomedical protein modeling at large (we'll provide more details in due time).

Crunching the whole set was a technical challenge per se. Volunteered power has grown a lot during the project. This may have been motivated by (1) the continuous availability of so many workunits; (2) shutting down SETI server; (3) the lockdown; (4) the notoriety of distributed computing for fighting COVID-19. This placed additional strain on the server, but in the end the mammoth task was completed - and we want more :)

T

15 May 2020 | 7:45:26 UTC · Comment

Project resumed
Disk occupation went down a bit, so I am un-suspending. 28 Apr 2020 | 10:12:56 UTC · Comment

Suspending project
I'm temporarily suspending the project to give time to empty the disk. 27 Apr 2020 | 14:51:57 UTC · Comment

Doubled number of hosts
If I am not missing anything, GPUGRID volunteers doubled the number of active hosts in the last month. It may have been either due to the closing of seti@home, or a consequence of folding at home’s covid effort.

(Credits: Boincstats) 23 Mar 2020 | 12:43:11 UTC · Comment

Server disk full being addressed
I'm working to resolve. Thanks for the support :) -T 22 Mar 2020 | 20:48:44 UTC · Comment

Outage resolved
Before anybody wonders: yes there was an another outage last night. Thanks for the patience. 13 Mar 2020 | 9:45:31 UTC · Comment

Experiment queue being filled up
There should be plenty of work in workunits of the "MDADpr4" series. It should be one of the largest efforts so far.
T 17 Feb 2020 | 12:09:59 UTC · Comment

Large scale experiment: MDAD
We are starting a new large-scale experiment. There will be plenty of workunits, whose very first batch is currently being sent. Run times should be around 6h but with a lot of variability. They are very heterogeneous so please don't worry for failures.

Thanks! -Toni 25 Jan 2020 | 10:07:33 UTC · Comment

Happy new year from GPUGRID...
...we may be late for the merry Christmas wishes, but not for wishing you a wonderful 2020 :)

The project scientists 27 Dec 2019 | 20:01:32 UTC · Comment

Disk full
I am aware of it and working to solve. No need to abort your workunits. I'm stopping the project in the meantime. 1 Dec 2019 | 12:02:56 UTC · Comment

New paper: Machine Learning of Coarse-Grained Molecular Dynamics Force Fields
I've computed (tentative) credits for the new methods paper https://pubs.acs.org/doi/10.1021/acscentsci.8b00913 ("Wang et al."). Congratulations to all co-authors, and especially Adrià and Gianni who did the GPUGRID work. WUs were named *CHIG*.

(Not in the "science" page yet).

26 Nov 2019 | 14:02:19 UTC · Comment

New workunits
I'm loading a first batch of 1000 workunits for a new project (GSN*) on the acemd3 app. This batch is both for a basic science investigation, and for load-testing the app. Thanks!

If you disabled "acemd3" from the preferences for some reason, please re-enable it. 21 Nov 2019 | 17:10:20 UTC · Comment

All acemd3 apps updated (210)
Currently there should be no major *known* bugs. We should cover Win64 and Linux, with reasonably recent cards.

Unfortunately, an internal cleanup in the filenames will make *existing* WUs fail. Sorry about that. Will send new test WUs soon.

By the way, the scheduler for this app will base its decision simply on the CUDA version supported by your driver, rather than other heuristics. 16 Oct 2019 | 10:47:28 UTC · Comment

Acemd3 restart on windows possibly fixed
The new acemd3 app should fix the issue.

Thanks for all the reporting!

Note that one still can't restart between different types of cards. 7 Oct 2019 | 13:38:53 UTC · Comment

More Acemd3 tests
We've uploaded Windows and Linux apps named "acemd3". If thing go as expected, they should be the new simulation engine. They should be an improvement on many aspects, especially maintainability and compatibility with RTX.

There were a few short test workunits (TONI_TEST). Larger one should come soon. Please be patient as we iron out the details. 6 Sep 2019 | 12:23:10 UTC · Comment

Acemd apps should be fixed
We are aware of the problem and working on it. Sorry for the inconvenience. 10 Aug 2019 | 18:17:30 UTC · Comment

Science non-stop: another paper, another badge
...and here's another badge for another publication issued in 2018, Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. This one is also on Sci. Rep., open access.

Here, the authors used Gpugrid-based simulations to reconcile experimental results on Dopamine D3 receptor antagonists with their molecular structures. They used the large-scale high-throughput molecular dynamics with Markov state models (MSMs) to determine an alternative and possibly elusive pose ("cryptic") consistent with the mutation data.

Thanks to every contributor!

Noelia Ferruz, Stefan Doerr, Michelle A. Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S. Marr, Robin T. Nelson, Bethany L. Kormos, Travis T. Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola & Gianni De Fabritiis
Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs
Scientific Reportsvolume 8, Article number: 897 (2018)

The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F6.52. Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.

13 Jul 2019 | 8:36:59 UTC · Comment

New badge, new(ish) paper
Dears,

we added a badge for a (not-so-recent-any-more) paper Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. The abstract is here and the text is open-access.

It is interesting because it provides evidence about the kinetics (i.e., transient conformational changes) incurred by the µ-opioid receptor (MOR) upon binding to drugs. MOR is part of the large and important GPCR protein family, which is targeted by approx ~30% of the current drugs.

Abhijeet Kapoor, Gerard Martinez-Rosell, Davide Provasi, Gianni de Fabritiis & Marta Filizola
Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity
Scientific Reports volume 7, Article number: 11255 (2017)

While the therapeutic effect of opioids analgesics is mainly attributed to µ-opioid receptor (MOR) activation leading to G protein signaling, their side effects have mostly been linked to β-arrestin signaling. To shed light on the dynamic and kinetic elements underlying MOR functional selectivity, we carried out close to half millisecond high-throughput molecular dynamics simulations of MOR bound to a classical opioid drug (morphine) or a potent G protein-biased agonist (TRV-130). Statistical analyses of Markov state models built using this large simulation dataset combined with information theory enabled, for the first time: a) Identification of four distinct metastable regions along the activation pathway, b) Kinetic evidence of a different dynamic behavior of the receptor bound to a classical or G protein-biased opioid agonist, c) Identification of kinetically distinct conformational states to be used for the rational design of functionally selective ligands that may eventually be developed into improved drugs; d) Characterization of multiple activation/deactivation pathways of MOR, and e) Suggestion from calculated transition timescales that MOR conformational changes are not the rate-limiting step in receptor activation.

9 Jul 2019 | 10:08:50 UTC · Comment

New acemd
HI,
we are testing a new application that will provide Turing support based on the new application acemd v3.

For now we have deprecated the linux version of v2 and we will soon release v3 for linux using a boinc wrapper.

If the boinc wrapper works, then it should be easy because the application works by itself and it has been tested extensively.

gdf

16 May 2019 | 15:49:46 UTC · Comment

Season's Greetings from Gpugrid!
We hope that the cold of the winter is at least a bit relieved by WUs crunching... to you all crunchers we wish a Merry Christmas and a happy New Year! 24 Dec 2018 | 20:00:58 UTC · Comment

WU: IAP
Dears,

I am sending a new experiment on the short queue targeting inhibitor of apoptosis proteins.

Inhibitor of apoptosis proteins (IAPs) constitute a family of conserved protein in the apoptotic pathway. In other words, they prevent the "programmed death" of cells; therefore, their over-expression enhances survival and resistance to anticancer agents. Small molecules (smac mimetics, SM), similar to the natural antagonist of IAPs, are a first generation of drugs which have been developed to sensitize cells to apoptosis. Although they are currently used in cancer therapy, there are some cases in which the SM-mediated degradation brings to the non canonical activation of NFkb and so to the expression of CIAP2 gene, suppressing TNF-alpha killing; in other words, resistance may arise to SM. In this set of simulations we are testing some mechanisms with which apoptosis in resistant cancer cells may be restored.

The WUs are tagged "*IAP*".

Thanks! 30 Nov 2018 | 15:17:54 UTC · Comment

Windows apps restored
We restored the windows applications.

If you get errors such as "197 (0xc5) EXIT_TIME_LIMIT_EXCEEDED", please try these:

- R̶e̶r̶u̶n̶ ̶b̶e̶n̶c̶h̶m̶a̶r̶k̶s̶
- Reset the project
- Wait the problem out

If nothing works and you want to fix right away, there is a more complex workaround editing client_state.xml

The problem is somewhat explained here. 27 Jul 2018 | 15:59:09 UTC · Comment

Windows GPU Applications broken
Currently we have the windows applications broken. We are looking into it.

Linux and CPU jobs work fine 17 Jul 2018 | 12:34:38 UTC · Comment

More CPU jobs
...with a new and improved application (Linux only). The current version should eliminate dependencies on gcc and devel libraries. 3 Jul 2018 | 11:59:53 UTC · Comment

More CPU jobs
Please remember that to run QMML jobs (linux only) you will need to install both the gcc and libc6-dev or glibc-devel (the latter depends on your distribution) packages. 6 Jun 2018 | 15:29:02 UTC · Comment

Attempting a fix for multiple CPU jobs starting at the same time
Application QC version 319 uploaded as an attempt to fix the problem. 6 Jun 2018 | 9:37:53 UTC · Comment

Phd position, please share it
http://www.multiscalelab.org/jobs/phd-machine-learning-computational-chemistry/ 22 Mar 2018 | 11:00:36 UTC · Comment

New publication: Molecular Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors
Hello everyone!

I just wanted to announce that our work on the chemokine CXCL12 has just been published (https://www.ncbi.nlm.nih.gov/pubmed/29481075) and badges have been distributed accordingly. I have updated the science page (http://gpugrid.net/science.php?topic=methods) and you should now be able to check your contribution to the work.

Thanks again your contribution and for making this project awesome!

Gerard M. 1 Mar 2018 | 16:10:07 UTC · Comment

The experimental QC for W10 is now called QC_beta
Another attempt... instructions here 20 Feb 2018 | 15:09:55 UTC · Comment

CPU jobs on Linux
Hi, we need more CPUs on Linux to run QM simulations. Anybody can help? 5 Feb 2018 | 19:30:27 UTC · Comment

Linux app failing
We will need to upload a new linux app soon to solve the expired current executable.

gdf 5 Feb 2018 | 9:20:29 UTC · Comment

New Student and QMML Project
Hello everyone and happy new year!

My name is Dominik and I am a masters student from Germany. I studied biochemistry in the city of Bayreuth, but I always focused my work more towards biophysics and bioinformatics. I'm in the group since October, where we have since then started to initiate a quantum chemical machine learning project.
We soon came to the conclusion that we need a quantum chemical database in order to drive research forward in this field.

This is where we need your help!

Some of you have already seen that I released a small amount of 50.000 WUs yesterday evening and there is even more. The WUs contain a certain amount of small molecules for which quantum chemical simulations will be performed. Depending on the size of the molecule the simulation (and the WU) will take longer. We did initial benchmarks to estimate how to design the WUs, but everything turned out a bit different with the very long WUs I prepared for Toni which you were fighting with over the last month. Thanks to everyone who was helping and sticking through this! I will try to adjust the WUs as best as I can, but for now the current DOMINIK WUs that are already on the server are fixed.
Regarding the windows based QM tasks I cannot give a clear answer about this yet, but it's definitely one of our goals.

It is a long term goal of ours to keep running the quantum chemistry tasks on GPUGRID and I try my best to ensure that there are always tasks available.

So thanks again to everyone who is participating and helping out. I really appreciate it very much.

Have a great start into 2018! 4 Jan 2018 | 13:44:42 UTC · Comment

Experimental QMML WUs
We are experimenting with CPU workunits. Right now they are Linux only. Please note that you may need to install "gcc" in your machine for them to work. More details in the Multicore forum! 19 Dec 2017 | 15:19:45 UTC · Comment

New multicore app and WUs
Dears,

we would like to test our new CPU multicore application for quantum chemistry tasks ("QC"). Since it’s the first time we have a CPU app out, I’ll test the behavior of GPUGRID with a relatively large batch that you will see soon. Workunits are named "*QC309big*".

Here’s some features of the app, in short (subject to change):

* Platform: Linux only for now, generic x64.
* Threads: as many as Boinc decides. I guess it depends on your machine, your preferences, and other running tasks in ways which are obscure to me…
* Run time: about 1 CPU hour per WU (so, shorter if multithreading)
* Credit: computed with the default algorithm (tasks are short, don’t expect much). Bonus mechanism for fast turnaround is still on.
* Known bugs: restarts and checkpoints. This should be mitigated with the “keep in memory when suspended” option. Sorry about that, it’s outside of our control.
* Network behavior: the first time you get a WU of this kind it downloads a Python interpreter (miniconda) and then some open-source packages, and installs them in the project directory. The installation is reused whenever possible.
* Disk usage: could go around 1 GB, perhaps more when tasks are running. Resetting the project should remove everything.
* Memory usage: should be around 1 GB when running.

Depending on the results of this test, we’ll start thinking about other platforms.

Thanks and nice crunching!

Toni 10 Nov 2017 | 14:58:07 UTC · Comment

New publication: High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD
Dears, we added badges for a recent methodological publication, High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD.

We describe a procedure to automatically set-up membrane simulations, and show it working en masse on all membrane structures published in the OPM database (hence the WU names you may have seen in the past).

Membrane proteins are quite interesting because they are involved in extra-cellular signalling, not to mention how many of them are drug targets; simulations are especially time-consuming to set-up, and we tried to develop tools to make the process less error-prone.

Thanks to all contributors! 9 Aug 2017 | 8:47:03 UTC · Comment

New publication: Complete protein–protein association kinetics!
Hey all,
some astute members might have noticed we got a new publication out? https://goo.gl/MoIi0d

You remember these BARNA/BNBS workunits? Well, we finally made it :)

Frank and Nuria did an incredible work with our simulations and got the paper published in Nature Chemistry which is a top-top journal in our field!

To thank you all for this incredible contribution we will be handing out badges soon and you have my (and our group's) heartfelt thanks to all of you!

ps. A layman news piece on the article https://www.upf.edu/home/-/asset_publisher/UI8Z8VAxU47P/content/id/8788860/maximized 12 Jun 2017 | 9:20:39 UTC · Comment

An important note for Windows XP users
Dear all,

GPUGRID will stop supporting Windows XP in April 2018

Every version of the science application we have to maintain costs us time and effort, and it's important that we focus our resources where they can give us the best return.

Building and testing Windows XP versions our applications is increasingly difficult now the OS is unsupported by both Microsoft and NVIDIA.
There are now fewer than 20 Windows XP machines crunching on GPUGrid, out of a total of over 2500, and it's difficult to justify on-going engineering effort for a small fraction of our capacity.

Sadly, this means that it's time for us to stop supporting Windows XP. The recent update to the application will be the last, and will cease to work one year from now. After that time work will only be issued to hosts running Windows 7+ or Linux.

If this affects you, please accept my apologies. Your contribution has been greatly appreciated, and I hope that you'll continue to support us.

Matt
17 Apr 2017 | 20:19:56 UTC · Comment

App update 17 April 2017
Dear All,

If you've been following other threads on the forums, you'll know that the Windows versions of the science application have recently been updated. There are now two versions, 849 (CUDA 6.5) and 918 (CUDA 8.0), which will be assigned to hosts as follows:

* 849
- Windows XP (32 or 64 bit) and any GPU >= sm 3.0
- Any 64bit Windows with a Kepler 3.0 device

* 918
- Any 64bit Windows, Vista or later with any GPU > sm 3.0 and driver >= 370.0

The peculiar exception for sm 3.0 devices is due to a compiler problem with CUDA 80 that affects only that hardware version. When that's fixed, hosts with a non-XP Windows will get 918.

If you see any behaviour that deviates from this, please report it here.

If you think you should be getting work, but aren't please check that your system complies with the above, in particular the driver revision and that the OS is 64 bit. 17 Apr 2017 | 19:49:15 UTC · Comment

New acemdlong app
Windows Version 915 is now unified for Kepler, Maxwell and Pascal.

No problems expected, bit report anything unusual here..

MJH 7 Apr 2017 | 21:36:55 UTC · Comment

Download problems. Can you help?
After some tests the only thing that we are sure is that downloads of large files stall when the operating is CentOS7. If we use CentOS6 they do work. Can anybody reproduce it?

the way we test it on gpugrid is:
wget --no-cache --delete-after http://www.gpugrid.net/download/libcufft.so.8.0

We don't know if it is a combination of CentOS7 and our network or it's a problem of CentOS7.

There could also be other problems but this is one.

gdf 23 Dec 2016 | 22:44:21 UTC · Comment

WU: BNBS
In case anyone is wondering what these WUs are, we are running some extra simulations on the Barnase Barstar system (previously called BARNA: http://gpugrid.net/forum_thread.php?id=3709#36142 ) to answer some questions of the reviewers. If the results get us through the review process this will be a major publication :) 21 Dec 2016 | 9:51:46 UTC · Comment

New server is running!
Post here any problem please 30 Nov 2016 | 21:35:53 UTC · Comment

Server going down for upgrade
Please be patient. 30 Nov 2016 | 9:12:53 UTC · Comment

Major server upgrade!
Dear cruchers!

the GPUGRID server you know and (I guess?) love has done a huge service to science. Thanks to your support, the experiments we have being running grew in size and scope... AND we have enough ideas for the future to keep this trend.

So, we decided to significantly upgrade the capabilities of our server - and a new is almost in place. Likely next Monday, we'll stop the server for some hours, then perform the transition. We now need your patience, because the switch-over will require some down time (and hiccups, possibly).

But we are definitely looking forwards for the new expanded experimental capacity! We'll keep you informed!

17 Nov 2016 | 10:48:09 UTC · Comment

PASCAL App Testing
Hello Crunchers,

I have just put out application version 900 for owners of Pascal GPUs. To test this you need:

* A Geforce 10-series or Tesla P-series GPU
* 64 bit Windows 7 or later
* NVIDIA Driver 360+
* Accept beta work, and WUs from the acemdbeta and acemdshort applications

Please report all problems in this thread. 27 Oct 2016 | 14:11:15 UTC · Comment

I'm a postdoc!

Hey! I guess I forgot to tell you guys, but better late than never :P
I successfully defended my Ph.D. on the 16th of September!
Now I'm continuing for a while as a postdoc in your good-ole well-known lab.

I would like to thank you all for making this possible! Without you* I would never have done all this cool research, publications and completed my thesis.

Many, many thanks and to further awesome research!

* and your awesome GPUs :D 25 Oct 2016 | 18:08:24 UTC · Comment

New badges!
Dear all!

We added badges for two great papers which came out this year. Both appeared in Scientific Reports, a highly-regarded open-access journal.

I don't think I can do better justice to the works than the author's own words, so I am copying here their abstracts, which hopefully convey the gist of the respective impact:

Noelia's study of ions binding to the myo-inositol monophosphatase enzyme:

Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic complex is well characterized, the binding process by which substrate, cofactor and protein cooperate is essentially unknown. Here, we have characterized cofactor and substrate cooperative binding by means of large-scale molecular dynamics. Our study showed the first and second Mg2+ ions identify the binding pocket with fast kinetics whereas the third ion presents a much higher energy barrier. Substrate binding can occur in cooperation with cofactor, or alone to a binary or ternary cofactor-IMPase complex, although the last scenario occurs several orders of magnitude faster. Our atomic description of the three-body mechanism offers a particularly challenging example of pathway reconstruction, and may prove particularly useful in realistic contexts where water, ions, cofactors or other entities cooperate and modulate the binding process.
Nathan's study of S1PR1 receptor:

The binding process through the membrane bilayer of lipid-like ligands to a protein target is an important but poorly explored recognition process at the atomic level. In this work we succeeded in resolving the binding of the lipid inhibitor ML056 to the sphingosine-1-phosphate receptor 1 (S1P1R) using unbiased molecular dynamics simulations with an aggregate sampling of over 800 μs. The binding pathway is a multi-stage process consisting of the ligand diffusing in the bilayer leaflet to contact a “membrane vestibule” at the top of TM 7, subsequently moving from this lipid-facing vestibule to the orthosteric binding cavity through a channel formed by TMs 1 and 7 and the N-terminal of the receptor. Unfolding of the N-terminal alpha-helix increases the volume of the channel upon ligand entry, helping to reach the crystallographic pose that also corresponds to the predicted favorable pose. The relaxation timescales of the binding process show that the binding of the ligand to the “membrane vestibule” is the rate-limiting step in the multi microseconds timescale. We comment on the significance and parallels of the binding process in the context of other binding studies.

Edit: The Science page does not contain the new papars yet, but you will find them in your profile page. WU names were respectively like 1mgx1, 1mgx2, 3mgx1, 3mgx2, 5MG, 20MG, 20MG2, INSP, INS1P (Noelia's) and RPS1 (Nate's). 20 Oct 2016 | 18:29:45 UTC · Comment

WU: CASP
Hey all. The next weeks I will be sending out some simulations starting with the CASP name. It will consist of a total of 3600 simulations running at any time (meaning that once some of them complete, new ones are sent to reach again 3600) probably for a month or so.
It will probably be my most thorough and organized method test so far so it should be fun :D

The simulations have their length written in their name (1ns, 5ns, 20ns and 50ns). Some will end up in the short queue and some in the long queue. Longest simulation time I measured on a 780 was 8 hours for one of the proteins at 50ns and shortest at 0.1 hour.

Right now I sent out the first protein called NTL9 to test if everything works as expected (so no 3600 simulations yet) but the next week I will probably send out another 4 proteins. So there should be lots to crunch in the coming days :) 13 Oct 2016 | 14:54:07 UTC · Comment

Disk full (solved)
One of the disks of the server is full, and the project is down. Apologizes for the problem! We are trying to fix it.

4 Oct 2016 | 16:06:11 UTC · Comment

New beta application
Hi Crunchers,

The eagle-eyed amongst you might have noticed the recent appearance of "Python Runtime" as the latest addition to our stable of applications.

* what is it? This app deploys a Python runtime environment based on the Conda python distribution.

* why do we need it? Almost all of our application development is now done in Python. This app will give us a way to reliably deploy and execute our software on GPUGRID volunteers' computers by providing a uniform, known Python environment

* how will it be used? If all works well, we'll be able to quickly test and deploy whole new applications, including replacements for the quantum chemistry and CPU MD applications we have previously experimented with. Being able to rapidly deploy new applications will markedly improve the rate at which our research group can innovate.

For the moment the app is Linux only but we hope to roll it out to Windows once it proves reliable.

Matt 30 Aug 2016 | 10:52:20 UTC · Comment

Geforce 10 / Pascal app coming soon
hi Crunchers

Just to let you know that there'll be a new app coming to support the ascal GPUs just as soon as Nvidia make a public release of CUDA 8.

Matt 22 Jul 2016 | 11:00:54 UTC · Comment

WU: OPM995 simulations
Here we go again :) This time with 33% more credits + corrected runtimes which means an additional 2x credit for WUs which take more than 18 hours on a 780 and only WUs which take up to a max of 24 hours on a 780. I hope I don't seriously overshoot on credits this time but it's really a bit hit & miss. 27 May 2016 | 8:54:11 UTC · Comment

WU: OPM simulations
Hi everyone.
Once again after a few years I have decided to simulate ;)

This is for a new project where I try to automatically build and simulate hundreds of membrane proteins from the OPM database http://opm.phar.umich.edu/ as a proof of concept.
But I will also keep an eye out to see if something fancy happens in those simulations which I am quite sure it will.

Membrane proteins are very interesting in general as they are involved in many diseases and are simulated quite often. So building a protocol to simplify this process would help lots of biologists.

For the moment I sent out just 100 simulations as a quick test, but in the next few days I will send out around 3000 equilibrations.

Beware! The simulations are very very different, so there is no point in comparing them to each other. I have some systems which run on the short queue in an hour and some monstrous ones which run on long for 10 hours. The credits are scaled accordingly to simulation complexity so no one will be cheated of his hard earned credits :)

Also keep in mind that the first batch will be minimization/equilibration simulations, which start the minimization by using the CPU for maybe 1 minute and then should switch to GPU for the equilibration.

I might post here some pictures of the systems as well because some of these proteins are just gorgeous!

Edit: I made some gifs for you here ;)
http://imgur.com/a/YbjOd 3 May 2016 | 15:08:28 UTC · Comment

New PhD student starting in June
Hi,
we finally have a new PhD student starting in June and another one by the end of the year.
So our usage of GPUGRID will raise again after June.

thanks.
gdf 28 Apr 2016 | 11:16:56 UTC · Comment

Noelia's PhD defence and departure
Dear all,

I have defended my doctoral thesis very recently, on March 4th, and it would have been impossible without your support. My thesis focused on the understanding of ligand-receptor interactions on a different set of systems, in all cases by running simulations in GPUGRID.

The thesis itself will be publicly available after an embargo period (here is the link in any case: http://hdl.handle.net/10803/363212) due to the still-unpublished works it contains. In summary, with the support of GPUGRID we have produced works on seven systems, three are already published, two under review and the two left will be submitted very soon (so expect new badges soon!!).

I must also say that I will be no longer working in GPUGRID. I have already moved to Boston where I will apply the methods that I have learned working on here to drug discovery programs.

Many thanks again,
Noelia 17 Mar 2016 | 2:48:37 UTC · Comment

New SSL certificates
I've just moved the project over to using Let's Encrypt certificates. Please post here if there are any connectivity problems

Matt 1 Mar 2016 | 13:16:03 UTC · Comment

*CXCL12_chalcone_umbrella* batch
Hi everyone,

yesterday we launched a bit more than 13,000 short WUs called *CXCL12_chalcone_umbrella*. They are pretty small WU, of 8ns (compared to a normal long WU ~40ns) and we hope they are easy and fun for you to crunch. Please post any problem you may encounter.

Scientists have been using a technique called Umbrella Sampling for some time now, with relative success in determining what we call binding free energy (which indicates how strongly a drug can bind its protein target). It is a pretty straightforward and much less expensive technique compared to the one we regularly use in our lab (adaptive sampling). However, it is particularly error-prone if the assumptions we take are wrong.

We are particularly excited about these WU, because while most scientific effort have been focused on reproducing free energies for single particular models or (most of the time) very simple toy models, it is the first time to our knowledge that, thanks to the fantastic community we have built together in GPUGRID, we can use this technique in a real case to screen potential drugs binding to CXCL12, a chemokine related to cancer metastasis.

Thanks to everyone for your contribution and I will be happy to assist you if you find any problem on the way. :) 28 Feb 2016 | 17:52:41 UTC · Comment

Linux app live again
I've just put out a fixed Linux app, version 847. Please report any problems here.

Matt 14 Jan 2016 | 15:48:45 UTC · Comment

do you have any experience with running a VM based application in BOINC?
There are projects giving out VMs instead of normal applications. We are considering it. How is it? Does it work?

thanks.

gdf 16 Dec 2015 | 23:55:12 UTC · Comment

Badges ready for the last paper!
Hello guys!

We recently published a paper which used a considerable amount of GPUgrid simulations. It would not have been possible without your contributions.

The paper is:

N. Ferruz, M. J. Harvey, J. Mestres and G. De Fabritiis, Insights from Fragment Hit Binding Assays by Molecular Simulations, J. Chem. Inf. Model., 2015, 55, pp 2200-2205

You can also browse ranking positions ;) :

https://www.gpugrid.net/science.php?topic=methods

Thanks to all!
Noelia 16 Dec 2015 | 11:06:55 UTC · Comment

Running low on WUs at GPUGRID
Hi,
somebody might have noticed that we recently running low in WUs.

The main reason for this is that we have very few people at the moment. Practically only Gerard is using it. Noelia is finishing her Phd in February and mainly writing up. Nate finished in July.

The good news that we are hiring more PhD students and already from January the group should be quite a bit larger with at least two other phD students and possibly one postdoc.

GDF 15 Dec 2015 | 8:08:12 UTC · Comment

Probable access problems on 9th Dec
On 9th Dec we are moving the IP of gpugrid to another network. This means changing the DNS. While the dns update is propagating around the world you might experience that the server is unreachable.

Early next year we are going also to upgrade the server, but this is another story.

GDF
1 Dec 2015 | 23:32:19 UTC · Comment

PhD position in machine learning at GPUGRID
http://multiscalelab.org/Jobs/Phd_neural_processing_learning_in_structural_molecular_biology

Please share in your network.

gdf 7 Oct 2015 | 21:21:45 UTC · Comment

Update to QC CPU application
Hello Crunchers!

Things have been a bit quiet on the GPUGRID development front for a while as we have concentrated on our scientific projects.
I'm now doing a spot of work on our new CPU quantum chemistry application, with a view to significantly increasing its use in the near future. Expect a flurry of updates (the first, version 101, is live now) - these are aimed at improving the platform support and performance.

Please note that this app is Linux only. It's unlikely that we'll be able to get a Windows version of this software built.

Matt

27 Jun 2015 | 12:30:39 UTC · Comment

Urgent PhD position at GPUGRID in Barcelona (please forward)
hi guys,
do you know anybody interested in doing a PhD with us. We have a fellowship but we need to find a candidate within a week.

Please forward it on if you know somebody interested
http://multiscalelab.org/Jobs/PhD_intrinsically_disordered_proteins_barcelona

Best,
gdf 18 Jun 2015 | 8:07:11 UTC · Comment

Server up and working
Yesterday and tonight we had a powercut. The sysadmin restarted the machine but he did not realize that apache was not running.

Now it should be all fine. 12 May 2015 | 15:55:24 UTC · Comment

Nathaniel Stanley's thesis and departure
Hello all,

This past Friday I defended my doctoral thesis, making me the second PhD to be produced thanks to GPUGRID.net. I owe you all a great debt of gratitude for supporting my work. My thesis covered my work on the study of complex binding processes in membrane proteins and disordered peptides. The membrane work was related to the enzyme FAAH and another work we are hoping to publish very soon. The disordered protein work was also a really great surprise for us, and will be continued further. The thesis itself will be published publicly after an embargo period (due to the still-unpublished works it contains). We will post the link as soon as it's available.

I must also announce that I will be leaving GPUGRID and moving on. I haven't accepted a position yet, but it is looking like I will be moving to a university in California in the next few months. It is a great opportunity and I'm very excited about it. I will continue to push forward biology with the methods and applications that I have learned working on here.

Thanks again and onward,
Nate 29 Apr 2015 | 10:29:48 UTC · Comment

donation page
We are currently fixing with the University admin people the donation page.

It should not take too long.

gdf 24 Apr 2015 | 7:50:29 UTC · Comment

Plenty of work
There is plenty of work now. Thanks for your patience.

gdf 20 Apr 2015 | 9:38:14 UTC · Comment

No work
We finished one of the storage filesystems and so new work units cannot run until this is fixed.

Of course it had to happen today. I am trying to fixing things up but it might take many hours because I am copying a lot of data out.

gdf 4 Apr 2015 | 23:35:55 UTC · Comment

New application: Quantum Chemistry
Hi,

I've introduced a new application, called "Quantum Chemistry".
We'll be using this to perform preparatory calculations on the small molecules that we simulate in our molecular dynamics simulations. This will help us to improve the quality of our simulations.

This app is restricted to Linux hosts with a processor that's SSE4-capable.

The first few WUs are failing, no need to report anything here just yet. I'm behind the curtain monitoring everything.

Matt 21 Mar 2015 | 14:56:04 UTC · Comment

Server performance
Let us know if there are still issues of connecting to the server or downloading/uploading.

gdf 4 Mar 2015 | 10:28:18 UTC · Comment

Server reboot
We rebooted the server today (after 1 year) to see if the recent problems are going to get better.

We are also planning to buy a new server as soon as we get some grant money.

gdf 4 Mar 2015 | 9:17:48 UTC · Comment

Change to CPU/AMD GPU application
To better reflect the nature of the application, the AMD GPU application is now called Molecular Dynamics for CPU and AMD GPUs.

It will be issued to any machine that:

* accepts CPU work
* has no NVIDIA GPUs
* has zero or more AMD GPUs

The intention is that it will use CPU cores, and be further accelerated by an AMD GPU is one happens to be present.

3 Mar 2015 | 18:44:25 UTC · Comment

New Beta app for AMD GPUs
Hi,

If you've an AMD graphics card, please subscribe to beta applications and see if you get the "amdmd" application. For now, it's just a place-holder, but this'll change soon.

Matt 27 Jan 2015 | 14:55:54 UTC · Comment

WARNING/CHALLENGE: VERY LONG WU (VERYLONG_CXCL12_confAna)
We just launched 400 very long WU (they will take about 24h in a 780GTX) named VERYLONG_CXCL12_confAna whose results we need as soon as possible (we are in a hurry). They come with a credit+bonus of 400K. Please, if you don't have a good graphic card, reject them. For the brave ones, take it as a challenge and see you on the performance tab ;) 22 Jan 2015 | 15:33:26 UTC · Comment

A new GPUGRID initiative
Crunching is a creative and challenging way of learning about the behavior of our computers and improving them while helping the GPUGRID team to understand a bit more the mystery of the world we live in and the diseases that affect not only us, but also the people we love. The GPUGRID team couldn’t be more satisfied and proud of forming part of this noble project, and so we’d like to deeply thank each of the 1000 users that connect to us every day, making us part of their lives and making them part of ours, as a team.

Behind each computer, behind each GPU and each WU or forum post, there’s the real protagonist of our story as a community: YOU, the cruncher.

At GPUGRID, we are considering the possibility of starting a new campaign to thank the users that contribute with our project by sending them little tokens of gratitude, such as proteins/aminoacid molecules printed by our 3D printer or merchandising such as t-shirts or stickers. We still have to establish the contest rules, but most likely each of the user would have a probability of winning based on their contribution. Once in a while we would like to run a story about the winner, explaining why you crunch, what's the setup of your computer, a small description of yourselves or a picture of you and your token.

We believe that it would be a fun and productive experience but before anything we’d like to know your opinion, your suggestions and whether we have your support for this initiative. Let us know! 21 Jan 2015 | 16:07:40 UTC · Comment

Important: No new work for pre-Fermi GPUs
Hello,

From today no new work will be scheduled to old pre-Fermi GPUs. This includes Geforce 8800, GTX200 series and GTX9800.

Matt 19 Jan 2015 | 17:30:40 UTC · Comment

Recommended driver 343 branch or higher
Happy New Year Crunchers!

Per the plans we announced last year year, the CUDA 4.2 application is now terminated leaving the CUDA 6.0 and CUDA 6.5 applications in production.

Henceforth, the CUDA 6.0 application will become the "compatibility" application, providing support to older systems. It will not receive any feature updates.

All new feature releases - new GPU support, performance improvements, etc - will be introduced in the CUDA 6.5 application. Baring any unhappy surprises, CUDA 6.5 will be our build platform throughout 2015 and into 2016.

As you can see from our statistics graph http://www.gpugrid.net/graphs/trend-appver.png , showing the fraction of our results produced by each application version, currently some 20% of our results are produced by the CUDA 6.0 application.

We'd very much like to reduce that to a minimum, so that as many people as possible are using the better application. To ensure you are getting the CUDA 6.5 application, please ensure that your NVIDIA driver is on branch 343 or higher.

Matt 13 Jan 2015 | 9:35:10 UTC · Comment

Happy crunchmas! (Gerard CXCL12)
We have fed GPUGRID with some new WU to keep you guys busy this christmas. This time we are simulating the binding of a small ligand to a protein called CXCL12, member of the family of chemokines. This protein appears to be altered in cancer and other inflammatory diseases. Happy Chrunchmas! 23 Dec 2014 | 13:43:09 UTC · Comment

Happy holiday season
Hopefully, a lot more GPUs and CPUs will join after the holiday presents.

At GPUGRID we are going away starting next week. The first to come back is Nate by the end of the year, early new year.

Also still remember that if you want, there is the possibility to make a donation. Donations are used to fund a PhD student which can work on Gpugrid. Last year we have received many donations. Thanks to everybody.

This year we also did well in terms of scientific publications:

N. Stanley, S. Esteban and G. De Fabritiis, Kinetic modulation of a disordered protein domain by phosphorylation, Nat. Commun. 5, 5272 (2014). pdf

G. Lauro, N. Ferruz, S. Fulle, M. J. Harvey, P. W. Finn, and G. De Fabritiis,Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods, J. Chem. Inf. Model., 2014, 54 (8), pp 2185–2189.

*** S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, J. Chem. Theory Comput. 10 (5), pp 2064–2069(2014).pdf

P. Bisignano, S. Doerr, M. J. Harvey, A. Favia, A. Cavalli and G. De Fabritiis, Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations, J. Chem. Inf. Model., 2014, 54 (2), pp 362–366. pdf

X. Huang and G. De Fabritiis, Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations, Adv Exp Med Biol 2014; 797: 107-114. pdf

** E. Dainese, G. De Fabritiis, A. Sabatucci, S. Oddi, C. Angelucci, C. Di Pancrazio, T. Giorgino, N. Stanley, B. Cravatt, and M. Maccarrone, Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH, Biochem J. 2014 Feb 1;457(3):463-72.

Almost all of these works have been made with your contribution. From next year we are also trying to have a larger impact in biomedicine, further developing new small molecules which can be used for treatment of disease.

Best,
gdf 16 Dec 2014 | 15:23:56 UTC · Comment

Discontinued CUDA 4.2 (update)
We had to discontinue cuda 4.2 apps because of some time limit in the executable.
As they were going to be discontinued anyway, we will only reintroduce it if really necessary.

If you were using cuda4.2, update your driver

* Discontinued CUDA 4.2
We need CUDA 6 to properly support the new Maxwell, so I'll be retiring the old CUDA 4.2 build. If you are still receiving version 4.2 WUs, please consider updating your driver to version 343 or above.
21 Nov 2014 | 10:47:01 UTC · Comment

WU: UBI
Hey all,
I am starting some new simulations whose names begin with ubi. They are relatively few so you might not notice them much around.
Essentially, after some success in folding the NTL9 protein (see previous WU posts) with a new method I was testing, I wanted to scale it up to a bigger, slower-folding (and more famous) protein and see how my method works on it. So here we go with Ubiquitin.
If this one is also kind enough to fold fast for me, we might be onto something quite useful :)

5 Nov 2014 | 13:50:55 UTC · Comment

New publication: Our study of a disordered protein and its significance
Hi everyone,

We are very pleased to announce the publication of our latest research article, titled "Kinetic modulation of a disordered protein domain by phosphorylation", which was published yesterday in the journal Nature Communications. You can see the official journal page link here. Since we know most of you don't have access to the fancy formatted version from Nature Publishing Group, we have placed the our less-fancy formatted pre-print version of the article here (first PDF link at the top of the page).

Since I am sure the title and abstract is quite cryptic/confusing to everyone, let me explain what we discovered and why this work was important. The main focus of the paper was a disordered protein domain called KID. Disordered proteins like KID do not have any rigid structures (so no x-ray crystal structures), and are in fact very flexible like polymers. However, despite being flexible they are very important and common in many different aspects of cell biology. They are important in many protein-protein interactions, such as ones that are important in communication inside the cell. They are frequently involved in many diseases like cancer (among many others).

KID is a protein that has been studied for more than 15 years, and a lot was already known about it. Other proteins in the cell chemically modify KID through a process known as phosphorylation, which then causes it to bind to specific proteins. It binds most famously to a protein known as KIX. The behavior of KID in the phosphorylated and normal state has been studied by a technique known as NMR (a cousin of MRI), and the binding of KID to KIX has also been studied this way. However, what we discovered in our study—and not seen by any other method yet—was that when KID is phosphorylated, it undergoes an a slowdown in its motions and forms a temporary, partially folded state. We believe this state is important in the binding process, and modelling and comparison with previous experiments also suggest this. This work is significant because it is the first time anyone has shown that such chemical modifications could change the behavior of a protein in this way, and also that it could have important consequences for the way proteins interact.

If you have questions, please ask away. We will assign badges and update the webpage soon. 29 Oct 2014 | 13:04:31 UTC · Comment

GPUGRID statistics graphs
Following up on the announcement to discontinue support for old hardware and the oldest application, here are two graphs showing the normalised throughput of GPUGRID broken down by compute capability and application version.

http://www.gpugrid.net/graphs/

The legends are messed up for some reason - the first graph is cc, {1.3, 2.0, 2.1, 3.0, 3.5, 5.0, 5.2 }, the second app version {42, 60, 65}

These will update daily.

Matt 16 Oct 2014 | 1:17:30 UTC · Comment

New CPU work units
I'm starting testing again on the "cpumd" multi-threaded CPU app. Please post observations here.

Matt 12 Oct 2014 | 11:53:16 UTC · Comment

Important: hardware and app deprecation for 2015 / ha-ha thread!
Hi,

With the arrival of Maxwell, we are now supporting 4 generations of hardware, and 6 separate builds of our application on 2 platforms.

This is starting to tax our resources, so some rationalisation is required. I therefore propose the following:

* Remove support for SM1.3
Geforce 200 series cards contribute rather less than 1% of our capacity and, furthermore, lack hardware features that we want to use in future development work.

* Discontinue CUDA 4.2
We need CUDA 6 to properly support the new Maxwell, so I'll be retiring the old CUDA 4.2 build. If you are still receiving version 4.2 WUs, please consider updating your driver to version 343 or above.

These changes will take effect from January 2015

Matt 6 Oct 2014 | 13:56:11 UTC · Comment

CUDA 6.5 app for Linux now available on acemdbeta and acemdshort
Experiences here, please.
4 Oct 2014 | 13:58:56 UTC · Comment

CUDA 6.5 app now on acemdlong
Matt 2 Oct 2014 | 21:17:15 UTC · Comment

Important news for GTX980 owners
If you are crunching with a GTX980 on Windows, please update your driver to 344.16

I am seeing a very high error rate for 980s with the initial driver release, 344.11

Matt 2 Oct 2014 | 21:04:20 UTC · Comment

New acemdshort app 846
I've promoted the CUDA65 app version 846 from beta to short.

You'll only get this if you have a Kepler or Maxwell card, and have a CUDA 6.5-capable driver, in practice rev 343 or higher.

Please post any problems or regressions here.

Matt 30 Sep 2014 | 8:32:04 UTC · Comment

New CUDA65 beta app
Dear all, please give the new acemdbeta app, ver 845, a work out. This supports all GPUs now.
It's Windows only - if you don't get WUs, you'll need to update your driver.

Matt 29 Sep 2014 | 9:49:51 UTC · Comment

Changes to scheduling policy
Hi all,

In attempt to rationalise the rules for assigning WUS to crunchers, I've made some changes to the underlying scheduler program. Here are the new rules:

* If you have a GM204 you will get a CUDA65 application, or nothing if your driver is too old

* If you have a Kepler or GM107 you will get a CUDA60 application, or nothing if your driver is too old

* If you have a Fermi card you will get a CUDA60 application if your driver is new enough, or a CUDA42 application if not.

Note that the CUDA55 application is retired.

A significant change is that we are now scheduling based on the CUDA version that the driver supports, rather than the driver version number. This greatly simplifies things on our side, as we no longer have to track the many different driver release branches. It does, however, expose us to problems if a driver incorrectly reports its capabilities. CUDA 5.0 and 5.5 were particularly bad for that, but I've not seen it for the 6 releases.

Matt 29 Sep 2014 | 8:09:51 UTC · Comment

Changes to scheduling policy
Hi all,

In attempt to rationalise the rules for assigning WUS to crunchers, I've made some changes to the underlying scheduler program. Here are the new rules:

* If you have driver >= 343.00 and sm >= 2.0 you will get a CUDA 6.5

* If you have driver >= 334.21 and < 343.00 and sm >= 2.0 you will get a CUDA 6.0

* If you have driver >= 295.30 and< 334.21 and sm >= 2.0 and < 5.0, you'll get a CUDA 4.2

* If you have driver >= 295.30 and sm == 1.3 you'll only get CUDA 4.2

Matt 29 Sep 2014 | 8:09:51 UTC · Comment

gpugrid.net layout upgrade
Hi fellows!

The GPUGRID team wishes you are having (or had) good summer vacations!

For September we are planning to release some changes in the web layout. Among others, extended statistic data will be provided so you can follow the progress of your contribution more closely.

We are still under development and we are open to any suggestions to make improve your experience as users. Specifically, we would be happy to hear which statistical data you find the most relevant or interesting and therefore susceptible of being displayed as graphs.

We thank you for your collaboration!

Gerard M. 29 Aug 2014 | 14:14:13 UTC · Comment

New CPU Application for testing
Hi,

There's a new CPU app available for Linux clients. A few WUs are out now, with some more to come after I've received the first results back.

The app is multithreaded, I think the default behaviour of the BOINC client is to allocate all cores to it.

Please report any observations here.

Matt

21 Jul 2014 | 21:07:26 UTC · Comment

WU: THROMBIN
Hi guys!!

There's a new project in the long queue ( NOELIA_THROMBIN ) . It consists of the binding of 6 different inhibitors to the protease thrombin, a protein in the coagulation cascade. With these, we are trying to demonstrate that molecular simulations can be as useful as X-Ray crystallography predicting binding modes.

Thanks to all,

P.D: Report any problems please!

Noelia 19 Jun 2014 | 17:03:08 UTC · Comment

WU: TRPS1S4
Dear all,

Just sent 1000 WUs under the group name TRPS1S4. This is probably the last batch of a project you've been crunching for more than one year now (WUs: FXA, FXArep.. and similar names) for thrombosis disease. This last batch is particularly important, since will allow us to see if these simulations can predict experimental outcomes. Please report any problems.

Thanks to all and happy crunching!
Noelia 11 Jun 2014 | 14:03:26 UTC · Comment

WU: CMYBKIX
Hi all,

I have submitted a bunch of new workunits to the short queue. This should fix the dry spell we have had there for the past week.

The workunits are named "NATHAN_CMYBKIX". In these simulations I am investigating the binding of a small disodered protein named cMyb to another protein named KIX. Disordered proteins and disordered domains (as opposed to nicely structured ones like hemoglobin) are very important in protein-protein interactions. Mutations in disordered proteins are very common in cancers, amyloid fibril diseases like alzheimer's and parkinson's, and probably a lot of other disease we don't know about. So, with these simulations we will be taking some first steps towards understanding some key things about these types of interactions. Lessons we learn from this system should help us work on many, many others.

Nate 31 May 2014 | 19:10:14 UTC · Comment

WU: BI_3
Hi all!

Just sent a new project to the long queue, around 2500WUs, ~100,000 credits each.
In particular, this project will help us to understand how antidiabetic drugs block its target, but also to develop a better general method for other targets and drugs involved in different diseases.

Thanks to all!! 19 May 2014 | 9:48:20 UTC · Comment

Important news for Linux crunchers
Hi all,

We are having a problem with correctly scheduling work to Linux clients because the BOINC client for that platform does not report the Nvidia driver version to us.

If you find that you are receiving the cuda60 application version and it is not working for you, the fixes are:

*) Upgrade to driver 334.21 or later

*) Try the patched (v7.3.15) client I have made available at:

http://secure.acellera.com/insecure/boinc/boinc (RedHat etc)
http://secure.acellera.com/insecure/boinc/boinc_ubuntu (Ubuntu)

(the patch itself is at http://secure.acellera.com/insecure/boinc/gpu_nvidia.cpp_patch )

This client reports the driver version and allows a correct scheduling decision to be made.

Matt 23 Apr 2014 | 8:11:22 UTC · Comment

Badges for two new papers
Dears, we have updated the badges to reflect two recent publications performed with your help:

* S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, submitted (2013).

and

* P. Bisignano, S. Doerr, M. J. Harvey, A. Favia, A. Cavalli and G. De Fabritiis, Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations, J. Chem. Inf. Model., 2014, 54 (2), pp 362–366.

You should be able to see them in your user profile, as usual. 22 Apr 2014 | 12:17:15 UTC · Comment

Please upgrade to DRIVER 334.21 or NEWER [closed]
Hi all,

As you may have noticed, we now have a CUDA 6.0 application. This brings with it several benefits over the older 4.2 and 5.5 applications, notably:

* Support for Maxwell GPUs
* Slightly improved performance
* Much lower CPU load

The minimum driver required for this app is 334.21, but any later version is OK.

In the longer term, our software development will assume CUDA 6. features, and it would be good to have as many of you as possible able to run it.

Currently 60% of all the WUs we get back are completed on machines with this driver or later (though many of you have been running the 55 app, because of our server scheduling policy)

If you have the opportunity, please do consider upgrading your driver!

Don't worry if you can't: the older applications aren't going away. From now on, though, they will get only maintenance updates.

Matt
21 Apr 2014 | 18:09:23 UTC · Comment

WU: BARNA
Hey everyone,
I am sending out some WUs to the long queue called BARNA (pun intended). The system we are investigating is Barnase/Barstar which are two proteins that interact with each other.
http://en.wikipedia.org/wiki/Barnase
http://en.wikipedia.org/wiki/Barstar

This will be (as far as I know) our first protein-protein interaction study and we are hoping to study some interactions like the ones in the crystallographic model and further develop the corresponding analysis tools.

7 Apr 2014 | 16:10:30 UTC · Comment

New CPU work units: 3HHM-1/ZINC
Hi gang,

The testing for the CPU application is over and these are the first production WUs.

In this project we are studying the PI3Kalpha, a mutation of which is implicated in tumor formation. You can read more about it, and see the structure, here: http://www.rcsb.org/pdb/explore.do?structureId=3HHM

Over the course of this project we will be testing some 22 million commercially-available drug-like molecules, drawn from the ZINC database http://zinc.docking.org/, to find compounds which are predicted to bind strongly to the protein in a way which will inhibit its function.

Once we have screen the whole database, we will take the best hits and test them for efficacy in a series of in vitro experiments. Hopefully we will find inhibitory compounds which can then serve as the basis for future drug development.

Matt 6 Apr 2014 | 10:38:57 UTC · Comment

Custom Android client
Dears, we are playing with a customized skin of the BOINC client. It attaches to GPUGRID by default (but allows you to add other projects manually).

Feel free to try the (unsigned) apk at www.gpugrid.net/download/apk/edu.berkeley.boinc.AndroidBOINCActivity.apk.

Let us know. 27 Mar 2014 | 15:54:43 UTC · Comment

WU: A2AR
A big hi to all the users! I'm currently undergoing my master thesis in the lab and I'll very proud to participate in this fantastic community for the first time by sending some simulations to gpugrid.

You will identify them with the ID A2AR, which stands for A2A adenosine receptor. It is a membrane protein from to a huge family called GPCRs that is key on neurodegenerative diseases such as Parkinson and therefore an important target of drug development. With these simulations we will try to prove the affinity of a couple of known ligands in silico. 26 Mar 2014 | 15:13:32 UTC · Comment

WU: CMYB_equil
Hello all,

I have submitted some simulations of a small peptide to the short queue. This is a special type of simulation, and it is also the first time I am running them, so there may be errors with them. Please let us know what you see. There should be pass through quickly, however, so hopefully they don't cause too many problems.

Nate 24 Mar 2014 | 11:02:08 UTC · Comment

New CPU WUs - DUDHIVPR
Hi All,

I've just submitted our first large batch of work units for the CPU application, named "DUDHIVPR*". The purpose of these WUs is to test the correctness of operation of our application by attempting to reproduce published benchmark data.

Matt 24 Mar 2014 | 10:38:10 UTC · Comment

Thanks to Anonymous for donation
Hi,
we have received a high donation from a person who likes to remain anonymous.

This message is just to thank this person. The money will contribute to pay a PhD student.

In the current economic situation we need more donations. Anybody who would like to contribute please do so using the donate link above.

GDF 21 Mar 2014 | 9:23:43 UTC · Comment

acemdlong application 815 updated for Maxwell
The cuda60 version of application version 815 is now present on acemdlong for those of you with the latest driver or a Maxwell card.

Matt 19 Mar 2014 | 16:59:44 UTC · Comment

New app on acemdbeta with Maxwell support
There's a new application on acemdbeta, version 811 for CUDA 60 which supports the Geforce 750Ti. You'll receive this app if your driver version is 334.21 or greater.

Please report problems here.

Matt

10 Mar 2014 | 10:58:32 UTC · Comment

Maxwell GTX750Ti
Hi Guys,

Just a line to say we've got our first GTX750Ti card up and running. The performance out-of-the-box matches a GTX480. We'll have a public app for GPUGRID just as soon as CUDA 6.0 is publicly released, which will probably happen at GTC at the end of the month.

Matt 5 Mar 2014 | 11:54:13 UTC · Comment

WU opi: Simulations on opioid receptors
Hi,
I have just submitted several hundred simulations on a collaboration study on opiod receptors. They are not much.

Any problem use this thread.

thanks,
gdf 5 Mar 2014 | 8:33:07 UTC · Comment

"Power To Give" - volunteer distributed computing for smartphones
HTC have just announced "Power To Give", a new BOINC-based initiative for volunteer distributed computing on Android smartphones. HTC deserve to be commended for putting effort into helping the development of a polished BOINC client for Android.

You can read all about it here: http://www.wired.co.uk/news/archive/2014-02/24/htc-power-to-give and see a video here https://www.youtube.com/watch?v=_0oJ39vs_Kk

GPUGRID's very own Gianni De Fabritiis presented at the launch, happening as part of the Mobile World Congress in Barcelona. Video to follow soon, but you can read as-it-happened coverage here http://www.gizmodo.com.au/2014/02/htc-mobile-world-congress-press-conference-live-blog-follow-all-the-news-as-it-happens/

We're very excited about this! Expect more news soon...

Matt
24 Feb 2014 | 23:17:46 UTC · Comment

Achievement: GPUGRID first project worldwide in boinc
At least yesterday GPUGRID was the first project worldwide according to BOINCSTATS.

Just a note to thank all the crunchers for contributing to our research.

gdf 20 Feb 2014 | 23:56:04 UTC · Comment

WU: NTL
I have submitted a thousand simulations try to fold a small protein called ntl9.
This is mostly a methodological work.

thanks for crunching,
gianni 17 Feb 2014 | 14:13:54 UTC · Comment

Uncovering the role of membrane lipids in modulating enzyme activity
Hello everyone,

At the end of last year, we updated the badge system to include several new publications we had just published. Today we want to highlight one of those pieces of work.

Starting in Mid-2011 (an eternity ago), we began collaborating with a research group in Italy to better understand something strange they had been seeing in their experiments. Specifically, they were seeing that when they modified the composition of lipids in a cell membrane, the activity of an enzyme named FAAH increased. They came to us to try to better understand why that was happening. Through simulations performed here on GPUGRID we discovered that, contrary to expectations, the lipids modified the function of the enzyme by directly interacting with it and its endogenous ligand. It had been expected that structural changes in the membrane would be the culprit, but that was not the case. Additionally, we report the first unbiased binding of a lipid to a membrane protein. This is one of the first experiments of this kind ever performed, and was possible only because of the compute power we have here at GPUGRID. You can read more about it on the science page here, as well as check out the video of the binding event.

Please note that (almost) all the papers we publish are available on our lab webpage. They can be found here. The versions of the documents there are the pre-print versions, basically meaning they are not formatted to look pretty. This is due to restrictions placed on us by the publishing companies. The text and figures are identical to those in the "pretty" version published in the journal, however. We are working on putting out copies of any papers missing from that page.

Lastly, we remind you that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated by all of you is greatly appreciated.

Thanks and onward,
The GPUGRID Team 12 Feb 2014 | 16:19:01 UTC · Comment

First low parts Maxwell GPUs out 18th Feb
GTX 750 and 750 TI will be out 18th Feb. These are based on the GM107 maxwell chip, so a small maxwell. Performance wise they should be around 40% the speed of a GTX780 but consume only 75W.

More details here.
http://en.wikipedia.org/wiki/GeForce_700_Series

We are going to Nvidia in US in few weeks, let's see if can get one to test.

gdf 7 Feb 2014 | 21:41:40 UTC · Comment

acemdlong application 815 discussion
I've promoted the version 815 application from acemdshort to acemdlong.

Post problems here, please.

MJH 23 Jan 2014 | 14:04:15 UTC · Comment

Plenty of Workunits to crunch
There are over 10,0000 workunits to crunch now at GPUGRID. Take your share.

gdf 21 Jan 2014 | 16:53:05 UTC · Comment

Off on Holydays
Happy holidays everybody,
we will be around but most of us are back for the new year.

There should be enough workunits to crunch since then.

gdf 20 Dec 2013 | 11:04:35 UTC · Comment

New Badges for four new articles
Hi everyone,

As some of you may have already noticed, we have updated the badges to include four recent publications. In other words, many of you should have new colored water badges with rankings in your profiles.

In the coming days/weeks we'll be updating the Science pages with details about the new publications, as well as posting here and on the Facebook page to give you all some background about the works.

If you have not received any badges in this round, please note that many of the workunits for this round were performed 1-2 years ago (inlcuding my infamous NATHAN_FAAH workunits, started in September 2011!). These papers have been a long time coming, and we are very glad to finally have the results published. Do not worry if you were not included in this round, because we expect to have another update in the coming months. Lots of good results in the pipeline, we are just trying to get them published.

Finally, just a reminder that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated is greatly appreciated.

And as always, thanks and onward.
The GPUGRID Team 21 Nov 2013 | 14:39:21 UTC · Comment

WU: NATHAN_benfix
Hey guys,

Minor group of workunits here on long queue. Just a small fix/check on some work we have sent for publication. You should barely notice them, and they should finish quickly.

Regards,

Nate 30 Oct 2013 | 18:57:29 UTC · Comment

WU: RL1_run
Hi all,

Just sent a bunch of ~1600 WU to the short queue. It won't last very long, only one step.

Thanks!!!
Noelia 25 Oct 2013 | 16:38:23 UTC · Comment

WU: FXArep
Hi all,

I have just sent a good bunch of WU (4000) to the long queue. Only two steps, 90000 credits each. With the analysis of this last batch, we will be able to finish a project on drug discovery for the thrombosis disease. Please let me know if you find any problem, although these simulations were already on the long queue some moths ago and should run fine.

Noelia 11 Oct 2013 | 14:16:34 UTC · Comment

Update to 331.40 to fix access violations on Windows
If you have been unfortunate enough to have been afflicted by the problem of repeated crashing with 'access violation' errors, please upgrade the Nvidia driver to 331.40 to rejoin us in the happy land of mostly-crash-free crunching.

MJH 8 Oct 2013 | 23:00:23 UTC · Comment

Access Violation Problems / Switching between WUs
For anyone getting the access violation problem, or very frequent switching between WU's, users of the forum have reported that the problem disappears with the new BETA v331.40 drivers.

See discussions:
http://www.gpugrid.net/forum_thread.php?id=3462&nowrap=true#33350
http://www.gpugrid.net/forum_thread.php?id=3498&nowrap=true#33384 8 Oct 2013 | 8:01:56 UTC · Comment

New Linux driver version 319.60 for 780s
If you are using Linux and have GTX780s, you should upgrade the driver to 319.60 to improve stability.

MJH 7 Oct 2013 | 17:39:47 UTC · Comment

WU: NOELIA_INS1P
Hi all,

New WUs in the long queue, big-box size, 120000 credits each. The batch has been previously tested and should not report any issues, but please comment any problems you might have.

Noelia 3 Sep 2013 | 16:31:37 UTC · Comment

acemdbeta application - discussion
The Beta application may be somewhat volatile for the next few days, as we try to understand and fix the remaining common failure modes. This will ultimately lead to a more stable production application, so please do continue to take WUs from there. Your help's appreciated.

Thanks,

Matt 2 Sep 2013 | 22:34:54 UTC · Comment

WU: NATHAN_KIDKIX...
Hi all,

Workunits with a similar name have been running for the past month or so on the long queue, but in keeping with our new policy I wanted to create a thread about them here. My original message in a previous thread was:

With these workunits, I'll be looking at the folding of a small peptide using a special force field. The biophysics community uses different force fields to represent the motions of proteins and other molecules, and we are attempting to test a new one so we can check some previous work and feel comfortable in work we are planning to do.

This work is a continuation of that, where we are now looking at the interaction of that peptide with another protein. The idea is to understand the interaction process, and later to see if the lessons we learn extend to other such interactions. There are MANY diseases in which these kinds interactions are important, from many cancers such as prostate cancer to neurological disorders like Parkinson's disease. They are fundamentally important to the function of cells. This is something I'll be looking at in the coming months.

If there are any problems or you have further questions, post them here!

Regards,
Nate 29 Aug 2013 | 11:01:31 UTC · Comment

Titan and GTX780 welcome
Hi,
with the new applications online for productions, we are happy to have Titans and GTX780 users on board.

IMPORTANT. Just make sure to have the appropriate drivers for these two cards (or newer):
http://www.nvidia.com/object/linux-display-amd64-325.15-driver.html
http://bit.ly/13k1Ajc
as these fix an important bug.

gdf 29 Aug 2013 | 9:59:42 UTC · Comment

WU: NOELIA_KLEBEs
So far I've had
one long wu error after 13s

one short wu complete OK
one long wu stall, ran for 2hr on a 660 but little progress, so got the bullet

Be on your guard!

29 Aug 2013 | 8:18:06 UTC · Comment

acemdlong application 8.14 - discussion
We decided to go live with the new application on ACEMD-Long.

It is version 8.00, and the server will automatically assign you a CUDA 4.2 or 5.5 version, depending on your driver version.

Any problems on this thread, please.

MJH 27 Aug 2013 | 15:59:45 UTC · Comment

Project servers up again
Problem with the database. Should be back online soon!

MJH

24 Aug 2013 | 11:45:14 UTC · Comment

WU: SDOERR_VillinAdapt
Despite its name, this protein is not villainous!
Similar technique as with BenAdapt but now with a different protein system. Lets see how fast we can fold this protein :)
I sent it to the long queue. Work units should take around 6.7 hours on a GTX 580

If you want to bask at its folded beauty (which I would hope to achieve) take a look at this rendering (not by our group): 23 Aug 2013 | 10:27:39 UTC · Comment

acemdshort application 8.15 - discussion
Dear all,

I'm working on putting out updated Windows and Linux applications that will have full support for 780s and Titans. If you have one of these card types, please sub to "acemdbeta" and try some WUs. The beta app version is 7.02 for both architectures.

Please post experiences here.

MJH 18 Aug 2013 | 13:02:34 UTC · Comment

WU: SDOERR_BenAdapt
Hey all, I will be sending under this WU name some workunits to test a new method that we are developing. If everything goes well it will allow us to simulate more "intelligently" allowing us to see even slower biological events.
Otherwise the system itself is of little interest as we have studied it before. These WU's are for testing the method as we know what to expect from this system. Therefore, the simulations will be very few and rare for the moment.

It's a heads-up in case you are one of the lucky few to get one of these WU's, hehe.

Edit: I forgot to mention, they should be relatively short for the long queue (estimated 3 hours on a 680) 14 Aug 2013 | 9:30:44 UTC · Comment

IMPORTANT: Patched Nvidia drivers for Titans and GTX780
If you have a titan or gtx780 please use these latest drivers from nvidia which fix an important bug.

Titan/780 drivers:
- Linux 325.15 http://bit.ly/13Qq4kf
- Windows 326.41 http://bit.ly/13k1Ajc

gdf 14 Aug 2013 | 9:09:54 UTC · Comment

Update on titans and gtx780s
Hi,
so an update is due with titans and gtx780s.
The current gpugrid application is not supporting it and we have not updated it for a reason.

At the moment Titans and GTX780s do NOT work. After a short time the application crashes. Nvidia has now recognized the problem and it is working on a fix for Titans which should be out in a month or so. It could be a new driver or a bios update.

For GTX780, the fix would be either together with the titan fix or it would not come for sometime or ever.

Best for crunching at the moment are GTX770.

gdf 19 Jul 2013 | 10:45:18 UTC · Comment

New group member ... new simulations
Hi guys,

I recently disembarked at the multiscale lab attracted by the high-computing facilities you all provide! I am an experience researcher in the structural biology field.

My first studies will be devoted to activate apoptotic proteins at atomic resolution, a family of proteins which control cell suicide and therefore are major players in cancer and neurodegenerative diseases.

S.
28 May 2013 | 16:33:25 UTC · Comment

New NATHAN_KID WUs on long
Hey guys,

I have put some new work on the long queue. These workunits are small and don't require any special algorithms, so should be no problems.

With these workunits, I'll be looking at the folding of a small peptide using a special force field. The biophysics community uses different force fields to represent the motions of proteins and other molecules, and we are attempting to test a new one so we can check some previous work and feel comfortable in work we are planning to do.

Happy crunching.

Nate 22 May 2013 | 17:30:20 UTC · Comment

New beta app for Titan owners
Hi,

If you have a Titan, please try out the new ACEMD beta application (You will need the option "run test jobs" selected too)

Please report any problems here on this thread.

MJH 20 May 2013 | 14:26:46 UTC · Comment

Canceled SDOERR WU's
I apologize for all whose WU's were cancelled today in the process of stopping the old ones and re-sending the new fixed ones.
At the beginning I didn't realize the effect and extend of the cancellation (since it was not intended to work this way), but I see now that many hours of computation and credits were lost due to this.
It seems to have been a bug in a script that had not been seen before until now, so we will refrain from using it until it has been fixed.
I realize that the computation time is very important for everyone so we hope that such hiccups won't happen too often in the future.

Many thanks for your patience and calculations! 16 May 2013 | 17:30:46 UTC · Comment

Titan and GTX780 support
We are probably merging the two updates at this point and update the applications to support titans and gtx780.

It all depends how long it takes to get gtx780.

gdf 15 May 2013 | 12:57:58 UTC · Comment

Donating via Amazon
Hey guys,

We've added a new way for users to donate to GPUGRID. We've set ourselves up as an Amazon Associate, and if you click the link in our donations page before making a purchase with Amazon, we'll receive some small percentage of the value of your purchase. This way you can make a donation while going about your normal purchases.

We are also considering updating the advertising banner(s) at the bottom of the page. We will likely keep it non-intrusive, non-annoying text, much as it is now. Certainly no flash animations.

As always, Thanks! 14 May 2013 | 15:49:22 UTC · Comment

New VIL workunits
Hi,
I have submitted some small workunits on folding. If they work fine, I will submit more, they are in the short queue.

gdf 13 May 2013 | 12:12:04 UTC · Comment

Deprecating Cuda3.1 application
As everybody moved to the cuda4.2 applications already, we are going to deprecate the cuda3.1 short queue.

gdf 29 Apr 2013 | 7:30:55 UTC · Comment

Old Noelia WUs
We have checked the error statistics and they are too high to be normal, so we are going to abort them.

They work perfectly over here, so it's not clear what is the problem. We might need to run few in beta to try to understand it.

gdf 7 Mar 2013 | 13:59:37 UTC · Comment

GPUs supported by the "ACEMD Long" application
Starting with this update to the ACEMD Long application, we are no longer supporting GPUs of compute capability 1.2 and lower. In practice this is everything below the spec of the GTX260 (8000-series, 9000-series, and low 2x0 and 3x0 cards).

There are two reasons why we are doing this:

1) It simplifies the application development because we have to support fewer hardware generations.
2) We are able to improve the specification of the Long WUs to better reflect the majority of the GPUs crunching them.

We are very grateful for everyone's contribution to GPUGRID, and I hope none of you with one of these older cards is upset by the exclusion. Work will still be available for you on the short queues.

Thanks all,

MJH 4 Mar 2013 | 18:49:48 UTC · Comment

New project in long queue
Hello all,

After testing the new application, it is time to send a new project. I'm sending at the moment around 6000WUs to the long queue. Credits will be around 100000. Let me know if you have any issues, since is the first big thing we submit to the recently updated long queue and these WUs include new features.

Noelia 1 Mar 2013 | 10:49:14 UTC · Comment

long application updated to the latest version
Among the advantages are reduced upload files. 27 Feb 2013 | 16:11:04 UTC · Comment

Final beta unit test
We have uploaded 100 workunits in the beta queue.

Please report any anomalies.

gdf 27 Feb 2013 | 8:19:13 UTC · Comment

For photos and videos
we will be posting photos and videos on the facebook page of gpugrid.

If you want to be notified just follow us:
http://www.facebook.com/gpugrid

gdf 26 Feb 2013 | 20:35:45 UTC · Comment

New WUs on Short 4.2 queue
Hey guys,

I have put about 1,000 new WUs on the Cuda 4.2 Short queue. In these simulations we're trying to get some information about the basic motions of proteins, and also study our force fields used to define their properties. The simulations are small and simple, so shouldn't suffer from CPU or memory issues. Happy crunching.

Nate

p.s. On the "Server status" page, the Cuda4.2 Short queue is actually the short queue on top. I will add some text indicating which is which. 21 Feb 2013 | 17:15:42 UTC · Comment

New app is out for testing
We have finished beta testing and we are now submitting workunits into a new queue for short runs.
If all works, we are going to update also the long queue.

Only cuda4.2 for the new app of course. Soon we will disable cuda3.1 as the application is way too old.

gdf 13 Feb 2013 | 21:44:34 UTC · Comment

βeta and short queue jobs
Hi guys!!

I will be sending a good bunch of WUs to the short queue during the following days. Group names "RC1_run" and "RL1_run". A total of 13624 jobs will be submitted in total, once the first step -currently ongoing in the betaqueue- is finished for each of them. Around 1200 already submitted.

Thanks a lot!!!! 7 Feb 2013 | 14:56:56 UTC · Comment

1Pflops milestone
GPUGRID has been constantly above the Petaflop in the past few days. Although just a symbolic number it feels good to reach such an impressive target for us.

Every volunteer should feel proud too, because it's all thanks to you.

gdf 3 Feb 2013 | 22:08:20 UTC · Comment

Beta testing starting soon
We will start some beta testing today or tomorrow with the new app for cuda4.2.
If it works we plan to update acemdlong.

gdf 22 Jan 2013 | 14:35:20 UTC · Comment

New tasks in the Short queue - Method validation
Hey guys,

I've put some new tasks in the short queue. These simulations are validation for methods development work we did previously. As you know, part of what we do at GPUGRID is develop new methods for running and analyzing simulations. These types of simulations are important because they help us learn how to extract information from simulations that are relevant for all kinds of biological systems in the future. For an overview of methods we've previously developed, go to the Science>Methods page.

Nate 9 Jan 2013 | 14:20:37 UTC · Comment

No longer cuda3.1 apps in acemdlong queue.
As announced we have deprecated the cuda3.1 application for the acemdlong queue.
The acemd2 queue stays with both applications.

From now on you should not be receiving acemdlong cuda3.1 apps.

gdf 2 Jan 2013 | 13:27:24 UTC · Comment

CUDA upgrade for long queue
Starting in the next few days we will remove the cuda3.1 application from the long queue.
If you want to crunch on acemdlong you need Nvidia latest drivers.

In a week or so, we wil also upgrade the applications to a newer version with mainly science related improvements, but also an output file of 1/3 of the current size.

gdf 31 Dec 2012 | 10:26:55 UTC · Comment

20,000 wus in queue New Year experiment
Hi,
so we have queued around 20,000 new wu in these days. This is unusual for us.

The WUs will last only two steps, so they should be all over by early January ready for analysis.
They look a lot, but in fact each is a much shorter sequence of other WUs which last for even 100 steps and take months to complete.

The idea is to have very many different runs which come back very quickly. Instead of taking months, we will take just weeks to do an experiment this way. Of course we need to see if the analysis says that it's ok.

As we never run so many and so long each step, we had some problems in the process. Some of which were visible, like the upload size too large and some were not visible to you (e.g. storage on server).

All this is also useful to learn and prepare the system to execute such large batches without problems.
The new application in January will also help in this.

thanks everybody and happy new year.

gdf 26 Dec 2012 | 10:20:48 UTC · Comment

New systems in Long queue
Hi all!

A good amount of new WUs will be around for the next weeks in the long queue. The systems are called hfXA_long and will provide around 90000 credits each.

Thanks and Merry Christmas to all!!
Noelia 19 Dec 2012 | 16:41:25 UTC · Comment

New PNAS paper has been published using results from GPUGRID
A great new paper entirely done on GPUGRID. Thanks guys.
http://www.imim.es/news/view.php?ID=159

Photos and comments on facebook:
http://facebook.com/gpugrid

gdf 4 Dec 2012 | 11:10:00 UTC · Comment

50 facebook 'likes' in one day
After one day, we are on our way to the target of 100 followers.

Thanks everybody. Please help us reach out new people so that gpugrid can grow.

gpugrid team 21 Nov 2012 | 7:46:07 UTC · Comment

New facebook page
www.facebook.com/gpugrid

Hi,
in order to communicate better our results, videos and images, we have now open an official gpugrid page.

This will help you to reach scientist and to discover what we do in an easier way.

Like the page for updates.

gdf 20 Nov 2012 | 9:30:35 UTC · Comment

New WUs on long queue
Hey all,

I submitted last week some new work units to the long queue. It's an old system, but new kind of simulation. We're working with an experimental group to see if we can reproduce some interesting results they saw. If we're successful it could give us more ways to find out important information about proteins. Of course, the results could also be negative, which is why we must do the experiment.

The work units seem to be running well right now. They seem to have a pretty low failure rate. Please let us know if there are any issues.

Edit: They have the name similar to NATHAN_benHP, for those that are interested.

Nathaniel 14 Nov 2012 | 14:36:50 UTC · Comment

CUDA upgrade notice
By beginning of next year, we would like to remove the cuda3.1 applications.
These are still the old apps and don't have several of the new features available in the new app which we need to do the science.

We will probably have a cuda4.2 app only, so within the next few months, drivers should be upgraded to at least this version. In our machines, the latest driver 304.51 works quite nicely under Linux, very robust.

gdf 3 Nov 2012 | 11:24:40 UTC · Comment

New systems in long queue
Hi guys,

Just sent a good amount of WUs to the long queue. Credits will vary from 60000 to 70000. Thank all for your time!

Noelia 11 Oct 2012 | 15:26:01 UTC · Comment

another sys on acemdlong
Hi,

I am submitting 500 WU on long queque of one of my last systems, that will be 57400 for each WU.

:)

Cheers,

Paola 25 Sep 2012 | 8:28:22 UTC · Comment

New WU on long queque
Hi guys,

I have submitted 500 WU of 69000 credits each.

Thanks for your computing time,

Paola 18 Sep 2012 | 8:15:27 UTC · Comment

Server problem fixed
The out of disk space error should be solved now.

Sorry for the inconvenience.

GDF 11 Sep 2012 | 8:13:11 UTC · Comment

hsp90 with high ligands concentration
Hi guys,

I am trying to enhance the sampling in a difficult system....hoping to improve the sampling HSP-90 chaperon.
I sent 500 WU on acemd long 76460 credits each

Thanks for your computing time,

Paola 21 Aug 2012 | 18:17:40 UTC · Comment

Lots of WU in short queue!
Hi guys,

It just finished uploading 14000 WU (same systems where in the beta queue last week) to the short queue. There are two types of systems and will provide either 1400 or 9500 credits each. Last week I posted half of these systems where going to be sent in the long queue, but we have more appropriate systems for this queue ready to be sent there in the following days -so expect high activity of your cards this week in both queues!-
These systems will allow to determine and ranking the best ligands within a large set of compounds for trypsin enzyme.

Thank you for your time,
Noelia. 20 Aug 2012 | 7:18:15 UTC · Comment

New system: amidotransferase
Hi guys,

I am submitting 500 WU, 14400 credits each on acemd short. The group name is 1XFG_HGA.

The system is an amidotransferase, that is involved in several biosynthetic reactions.

Cheers,

Paola 10 Aug 2012 | 10:41:34 UTC · Comment

More acemdbeta
Hey guys,

Be expecting a good bunch of workunits in acemdbeta!! ( around 14000). As before, this is not that we want to test the system, this is already the real thing that can only run in the beta queue. The systems are short and will provide either 3000 or 450 credits.

Thanks!
Noelia 8 Aug 2012 | 16:38:23 UTC · Comment

ENDOCHITINASE in complex with a purin derivative frag
Hi guys,

I am submitting 500 WU, 21800 credits each, on acemd short queque. The system is a chitinase in complex with a purin derivate. Chitinase hydrolyses chitin, an essential fungal cell wall component, playing a role in cell wall morphology, so inhibitors should have antifungal properties.

Thanks for your computing time,

Paola 8 Aug 2012 | 8:04:35 UTC · Comment

new system trypsin mutant L99A
Hi guys,

I am submitting 500 WU (17900 credits each). The protein is a trypsin mutant, to see if and how that mutation (Leucine 99 substituited by Alanine) affect the binding to benzamidine, following Ignasi's work :D

Paola 2 Aug 2012 | 7:28:47 UTC · Comment

EXOGLUCANASE I bounded to an amphipathic fragment
Hi guys,

I have submitted 500 WU with group name 1H46_RNP on acemd(short), 21600 credits each :)

Cheers,

Paola 30 Jul 2012 | 7:08:23 UTC · Comment

New system in beta queue && long queue
Hi guys!

I've just sent 500 WU to acemdbeta with 5250 credits each for the first phase of the simulations. This equilibration step can only be done in the beta queue, so this is not a test, but already the real simulation.
Once all this WU are finished I will be able to prolong all them in the long queue, giving a total batch of 3500 WU with around 50000 credits each, likely in the next two days.

The new system have already been in gpugrid: it is the domain SH2 but focusing on the interaction with fragment(s) and not with polypeptides as before.

I will keep you updated once I send the second part!

thank you ;)
Noelia 24 Jul 2012 | 15:15:18 UTC · Comment

Finding the best receptors
Hi all,

I submitted this afternoon a set of new systems to acemdlong with credits ranging from 40000 to 70000. This will allow to check which are the best binding candidates in a family of receptors for a given drug, and ultimately, extend the method to other families.

Thank you all for your computational time.
And have a nice weekend!!!

Noelia. 20 Jul 2012 | 21:48:36 UTC · Comment

New systems in beta queue
Hi all,

I just sent 500 WU on acemd beta, half of them with 450 credits and the other half 3000, only for the equilibration step. So this is a perfect occasion to check how the beta queue works ;). Once this is finish I will sent the complete simulations. This will allow to compute the energy of binding for about one hundred of different ligands to trypsin, and if this works, we'll extend to more than one thousand!!

Noelia. 19 Jul 2012 | 12:38:41 UTC · Comment

new system THYMIDINE KINASE- HYDROXYPROPYLADENINE
Hi guys,

I am going to send a new system, a THYMIDINE KINASE in complex with an adenine analogue inhibitor
500 WU on acemd short, 21700 credits each
and if it works fine, I will send asap even the complex with the enantiomer :)

cheers,

Paola 13 Jul 2012 | 18:02:01 UTC · Comment

Welcome to Noelia
Hi,
Noelia will start a PhD with us at gpugrid, so she will be sending you lots of work very soon.

We will be uploading pictures and descriptions soon.

gdf

10 Jul 2012 | 13:11:47 UTC · Comment

New 40% faster applications are now fully deployed
The new cuda4.2 applications are now fully in use for Kepler and Fermi.
cuda3.1 applications will still be given out if you have an older driver.

gdf 6 Jul 2012 | 9:34:50 UTC · Comment

New system submitted beta-lactamase
Hi dear volunteers,

I submitted tonight 500 WU on acemd (short) 12500 credits each.
The system is a beta-lactamase in complex with a negative charged fragment.

cheers,

Paola

p.s. sorry for the delay of the post....I am on vacations, but still thinking about work :) 5 Jul 2012 | 0:06:48 UTC · Comment

Farewell
Dear crunchers,

My time has come. Now that I got my PhD I must move on. I am leaving the lab and therefore GPUGRID.net as scientist although I'll be following it closely from wherever I am.

It's been a pleasure to work with you all and I hope you still keep your volunteering spirit for the years to come. You're really the fuel of the scientific project behind.

Thank you very much.

All the best,
Dr. Ignasi Buch 2 Jul 2012 | 17:04:46 UTC · Comment

let's sample the binding site....
Hi all,
I am submitting 450 WUs on acemdlong, 53600 credits each.
The group is ADAPT. I want to improve the sampling in the binding region.

Thanks to all for your computing time,

cheers,

Paola 29 Jun 2012 | 8:57:44 UTC · Comment

Ignasi's thesis defense TODAY- streamed online!
Guys,

I am told that in this address http://84.88.71.16:8080/auditori and using Windows Media Player, you can follow my thesis defense today scheduled at 15:00h Barcelona time (UTC+2). Double check your time difference, just in case...

Sorry for the short notice,
i 29 Jun 2012 | 8:00:14 UTC · Comment

New CUDA4.2 applications are out for Kepler GPUs
We have finally uploaded the new applications for Kepler supporting cuda4.2.

You should be receiving them if you have a recent driver. The new applications are substantially faster.

gdf 25 Jun 2012 | 9:23:16 UTC · Comment

3EKO_8LIG 3EKO with high ligand concentration
Hi all,
I am submitting 500 WUs on acemdlong, 53900 credits each.
The group is 3EKO_8LIG. It is the same protein target of my previous runs, a molecular chaperon (HSP90) involved in many cellular functions. I put an high concentration of the small ligand in order to improve the sampling.

Thanks to all for your computing time,

cheers,

Paola
~ 11 Jun 2012 | 8:26:43 UTC · Comment

Plenty of WUs in queue!
Guys, there are some big nice simulations waiting for you to come crunch them! 30 May 2012 | 10:37:06 UTC · Comment

New task on long queue from Nate, named RSP1120528
Hey everyone,

I have submitted some new tasks to the long queue. This is a new system that hasn't been run before on The Grid, but since I'm not doing anything new configuration wise, I don't expect any problems. These will be higher priority tasks than most, and if all goes well we hope to get some positive results quickly. I'll elaborate on the goal of these simulations later. They should run for about 7 hours on the fastest cards. I'll be keeping a close eye on them over the next few days, but please report any problems when you see them.

Nate 28 May 2012 | 16:20:08 UTC · Comment

Install new drivers for new application
The new application will soon make it to production.
You need to have the latest drivers to use it, because it is compiled with cuda4.2.

Linux: 295.41 or greater
Windows: 301.32 or greater
25 May 2012 | 17:26:57 UTC · Comment

This is what *xTRYP* WUs were about
Check this video out.

We are already working on the publication with the Dr. P. Carpentier the crystallographer from the ESRF Synchrotron in Grenoble (France) who's been able to crystalize some of the intermediate states of benzamidine binding that we see in our simulations.

cheers,
ignasi 24 May 2012 | 12:19:30 UTC · Comment

3EKObis another conformation
Hi all, I am submitting 500 WUs on acemdlong, 56000 credits each. The group and name are 3EKObis...because I have already completed one, but we need more data and I hope that this new conformer should give better results.

The system is a molecular chaperon involved in many cellular functions.

Thanks to all for your computing time,

cheers,

Paola 16 May 2012 | 13:45:22 UTC · Comment

Ignasi's PhD thesis
Dear all,

I finally have my thesis printed.
I thank you all (once again) for your crucial contribution to it. And of course, Gianni, Toni, Kashif, Matt, Nate and Paola for many many reasons.

The defense is programmed for the 29th of June and you are all invited if you can make it to Barcelona. Drop me a line if you really want to come. There shall be a party :)

cheerios,
i 9 May 2012 | 10:21:00 UTC · Comment

Problems with fragxa4 and fragxa3 WUs
We had to cancel these WUs on-the-fly. fragxa3 were 10 times longer by mistake and would not have finished in most computers.
On Monday we will look into compensating who was affected by this.

Sorry for the inconvenience.

gdf 22 Apr 2012 | 17:11:19 UTC · Comment

New *xTRYP* WUs
We are submitting a new batch of WUs (~1000) of our beloved trypsin and benzamidine system for a beautiful experiment in collaboration with a crystallographer.

It seems that these crystallographers and us may have got to similar conclusions on how trypsin and benzamidine like to interact. The nice thing is that we'd have got to the conclusions from VERY different approaches. They make crystals of trypsin/benzamidine and take pictures of their structures using a synchrotron and we make MD simulations of already solved structures and take many snapshots of what happened. And then we compare them.

If experimentalists (protein crystallographers in this case) are able to reproduce what we obtained from computer simulations or viceversa, it would be a beautiful (and necessary) validation of our methods.

Let's hope that all goes well.

Cheers! 18 Apr 2012 | 9:34:13 UTC · Comment

New WUs of TRYP (*adTRYP*)
We have submitted a new batch of TRYP (*adTRYP*), significantly longer than the latest TRYP (met*, eth*, pro*,...).

The latest TRYP were a real production attempt to straighforwardly obtain binding for small inhibitor molecules. It finally proved harder than first expected, therefore we are improving the underlying analysis method as well as implementing a cleverer scheme to obtain the data. That is what *adTRYP* are for, to prepare a systematic methodological study on how to produce efficiently many events of binding for small protein inhibitors. See experiments section for more info.

Cheers 2 Apr 2012 | 13:03:47 UTC · Comment

Tests on GTX680 will start early next week [testing has started]
We are looking forward to testing the new nvidia architecture. We will report the performance soon and really thank one anonymous cruncher for the donation.

gdf 23 Mar 2012 | 9:42:40 UTC · Comment

New GPUGRID team member
It is a pleasure for us to introduce you Paola Bisignano, PhD student at IIT (Italy) that is visiting us for 9 months. She has already started to send WUs to the queue, so soon you will be getting them.

Her work is similar to ours (i.e. *TRYP*) where we try to predict small molecule binding affinities and kinetics to protein targets of biomedical interest.

21 Mar 2012 | 18:42:34 UTC · Comment

New publication, new badges!
Dears!

We have recently published a new paper on the Journal of Chemical Theory and Computation: "Visualizing the Induced Binding of SH2-Phosphopeptide", authored by me, ignasi (shared co-authors) and GDF. In the paper we have made (hopefully :) good use of your donated GPU time to find out in detail what happens when a kind of signal is transmitted between proteins in a cell. The signal is the recognition of a short peptide (pYEEI for friends) by a partner "plug", called the SH2 domain. This kind of signaling is in fact very common in cells for responding to all varieties of messages (for example in receptor kinases).

We updated the badges accordingly - and this time we also briefly go down the hall of fame. Of the 3113 contributors, these are the 10 users who contributed the most computation (rank, name, millions of credits):

1 Retvari Zoltan 70.1
2 Venec 66.8
3 davidYuen 49.0
4 WirelessDude 46.8
5 Stoneageman 46.3
6 CTAPbIi 26.0
7 Helmholdt 24.8
8 Nikke 24.3
9 CNT - IQE 24.0
10 Ketzer7 24.0 19 Mar 2012 | 15:02:58 UTC · Comment

Update to FAX3 tasks on long queue
see details here: http://www.gpugrid.net/forum_thread.php?id=2903&nowrap=true#23933 13 Mar 2012 | 21:06:21 UTC · Comment

New task on long queue, significantly longer than traditional tasks
Hi all,

I have submitted some new work units that will replace some I submitted earlier in the week. The names will be "NATHAN_FAX3". These tasks are in the true spirit of the long queue, and will take about 12+ hours on the fastest cards. Some have already been returned and indeed have been around 13 hours. This is markedly longer than what you have expected traditionally, but we really want the long queue to be for critical tasks, computationally intensive tasks, and the like. I suggest you all take note of how these tasks run on your computers and be mindful of temps and errors as you start to receive them.

I have noticed some crunchers expressing concern/dismay that perhaps they will not be able to get the 24h bonus with such long tasks. We are mindful of that concern, and will keep an eye on this group as an experiment. If we think it is too unfair to people with fast but not the fastest cards, we'll be sure to correct that in future groups. But the less send/recieve we have to do, the better. We are also mindful of the fact that longer tasks might be more susceptible to errors/crashes, and we want to see how this goes. I'll be looking out for the severe error percentage over the next few days for any problems.

Also, a note about tasks beginning with NATHAN_FA... These tasks are unique in that they are quite large simulations, compared to many others we have done in the past which are smaller (bigger biomolecules mean bigger simulations). They not only take longer per step, but require more memory. Cards with lower memory (below 1GB) may suffer additional performance loss. There is nothing we can do about this, unfortunately.

Happy crunching.

Nate 10 Mar 2012 | 20:05:30 UTC · Comment

Server back online after power cut
We are attached to a temporary powerline, so we need to restart sooner or later to attach it to the proper one.

gdf 6 Mar 2012 | 11:42:25 UTC · Comment

Do not use 295.x driver on windows
The driver causes CUDA WUs to fail - here and on other projects. Please don't use it until NVIDIA fixes the bug. 5 Mar 2012 | 14:25:25 UTC · Comment

New wus on long, old project that needs validation.
Hey crunchers, I have put a batch of work units in the long queue that should make up for the drought. The work units themselves are not from a new system, but rather are an important validation of work I have already been doing. These work units require the long queue, and will likely take 12 hours on the fastest cards. Let us know if you have any problems or concerns and we'll do what we can to address them. 5 Mar 2012 | 11:09:12 UTC · Comment

acemdlong also updated now
The update process is finished also for acemdlong.

gdf 4 Mar 2012 | 17:52:03 UTC · Comment

New application acemd2 6.16 (WIN/LINUX)
We have upgraded the acemd2 application to get some features which we need in order to execute new WUs.

Soon, we will upgrade also acemdlong.

All the rest in the application stays the same and you should not notice any change.

gdf 4 Mar 2012 | 13:10:38 UTC · Comment

monitor suspend/resume bug in 295/296 drivers
There are some reports of bugs concerning the latest NVIDIA drivers (failures when monitor goes to sleep). GPUGRID may not be immune to the bug. If it occurs to you, either

* rollback to previous drivers
* or configure the monitor so that it does not turn off 24 Feb 2012 | 21:49:03 UTC · Comment

New TRYP WUs
I am submitting 700 WUs in the long queue as part of a new experiment.
You'll note that they have the TRYP tag that was used for our publication in PNAS 2011:
metTRYP
ethTRYP
proTRYP
isoTRYP
butTRYP
penTRYP
hexTRYP

We are now extending the study to 7 different ligands to see if we can reconstruct their bindings too.

cheers,
i 16 Feb 2012 | 15:53:51 UTC · Comment

AMD GPUs are now usable at Donate@Home, a different project from GPUGrid.
For running AMD gpus please check this thread:
http://www.gpugrid.org/forum_thread.php?id=2839

9 Feb 2012 | 0:00:05 UTC · Comment

New WUs: GIANNI_FR1
This is a set of 600 WU in the acemdlong queue related to method development.

gdf 7 Feb 2012 | 14:24:11 UTC · Comment

New wus on the long queue
We have put some not-so-long WUs in the (currently empty) long queue. They give normal credit (possibly with bonuses). This is part of an experiment to verify whether we can get low-latency results.

They are named "TAKExx". 7 Feb 2012 | 11:35:35 UTC · Comment

New batch of WUs: KKAL4
I've created around 1000 new WUs on the "normal" queue. They give 9100 base credits each. The type of WU uses a standard setup and we already had them around in the past. 6 Feb 2012 | 14:50:16 UTC · Comment

New windows beta application is out
Same as Linux which was fine. If it works we will update the production apps.
Again only minor changes.

gdf 27 Jan 2012 | 11:50:10 UTC · Comment

New acemd linux beta test app
A new app is up for test.
Only minor revisions.

gdf 25 Jan 2012 | 23:53:36 UTC · Comment

Badge system up and running!
You are seeing it :). Check your Account page too. 23 Jan 2012 | 12:30:50 UTC · Comment

Ladies and gentlemen, the GPUGRID Badges!
The Amino acids, components of proteins, the main characters in GPUGRID simulations. Given per total number of credits and milestones in 20 levels, the number of amino acids encoded by the universal genetic code (ordered by molar mass ~weight). Amino acid/credits equivalences below.

The Waters, basic component of life and a distinctive trait of our long and accurate simulations. 7 levels (Plastic, Bronze, Silver, Gold, Ruby, Emerald, Sapphire) to represent relative contribution to our scientific publications. Each water badge will be linked to the corresponding publication and Science topic. Water/percentage equivalences below.

The donor badge is changed to the crown

The complete information is available in the Volunteers page. We will update the server at the start of next week! 20 Jan 2012 | 14:52:37 UTC · Comment

More workunits in the long queue
Dears, we're sending 1000 more WUs related to the modeling of neural system.

These are named TONI_FAAEAC1 and TONI_FAAEAN1. They should give out 47700.9 and 36228.6 credits respectively.

As always, make sure you disable the "acemdlong" app in your GPUGRID preferences if you don't have one of the latest cards.

Toni 16 Jan 2012 | 19:10:07 UTC · Comment

GPUGRID's new Badge System coming soon
This is the first formal announcement for the new Badge System. Next week, we will unveil the badge images, although the final implementation may still take two or three more weeks. We can already tell you that there will be two types of badges: one for the total number of credits (one badge per user) and one to acknowledge the relative contributions on our publications (one publication, one badge). More soon! 13 Jan 2012 | 17:33:54 UTC · Comment

Web shortcuts in the Boinc client
We have added BOINC-client shortcuts to commonly-accessed GPUGRID web pages. (Known as Client Web Links or GUI Urls in BOINC lingo.)

You should soon see the following buttons appear in the Projects/GPUGRID tab: Your account; Your team (if any); Server state; Donations; Science; Forums.

Best wishes for a great year 2012!
9 Jan 2012 | 13:20:21 UTC · Comment

Happy Holidays!
GPUGRID wishes you Merry Christmas and a Happy New Year 2012. We hope the world doesn't end in 2012 as we've got lots of work to do! 23 Dec 2011 | 17:01:06 UTC · Comment

HIV research update
There has been further project development in the HIV research line which you may find on the Science page of the website.

I would also like to personally thank all volunteers for their continued support of this research. Thanks to your crunching we have been able to uncover one of the fundamental processes in the maturation of HIV. Some further computing is required to complete the work (Tag: HIVPR) and we look forward to your continued support in the future. 20 Dec 2011 | 14:21:01 UTC · Comment

GPUGRID has a new website!
Guys, you are seeing it.

Thanks to the awesome work done by Ignasi, GPUGRID.net has a new, stylish, (even steelish :-) appearance. The redesign affected essentially all the areas of the website.

We (well, Ignasi) has paid especially close attention to the "Science" section - it's completely redesigned, and includes visual cues of the each major area we are doing research in. We hope you will enjoy it!

Needless to say, the forums and user/task/WU/server status pages are also updated and in sync with the new style, but they maintain all the old functionality. The BBCode thing is now functional. For more details, comments, etc., please refer to the "server and website" forum.

A whole-hearted thank you to Ignasi for this Christmas present to the group.

Toni 20 Dec 2011 | 10:15:16 UTC · Comment

New work units on long queue
Hi all, I have submitted 1000 new workunits to the long queue. The simulations focus on the receptor CB1, and with them we hope to gain some insights that will have important implications for a wide range of diseases, including several neurological disorders, gastrointestinal disorders, pain, and cancer.

17 Dec 2011 | 16:19:03 UTC · Comment

Workunit distribution normal
WU and credit distribution should be normal now. Thanks for the patience. Feel free to report irregularities and concerns in the "Server and website" forum. 15 Dec 2011 | 11:48:22 UTC · Comment

First part of server upgrade complete
We upgraded the server software - if WU distribution, reporting, etc. is confirmed to work correctly, on Monday we will update the web pages.

As a first consequence of the upgrade, you should be receiving "notifications" in your BOINC clients. 14 Dec 2011 | 15:34:07 UTC · Comment

Server upgrade started
GPUGRID.net will be down for several hours. Follow us on http://twitter.com/gpugrid! 14 Dec 2011 | 13:45:22 UTC · Comment

Server upgrade imminent
Dears, just another reminder that we'll soon be upgrading the server software. There will be some down-time.

Even though we planned the transition carefully, we can't anticipate exactly how long will it last (hopefully in the order of hours). Feel free to increase the work cache.

T
12 Dec 2011 | 9:14:08 UTC · Comment

Winter is coming
A totally renewed version of the GPUGRID website will be soon released together with a server update. More news to come. 2 Dec 2011 | 11:57:10 UTC · Comment

@gpugrid Twitter account
GPUGRID finally goes social. We will be posting the News and other stuff through our Twitter account. We encourage you to follow us. Should be specially useful to communicate with you if the site is ever down. 18 Oct 2011 | 13:49:42 UTC · Comment

New workunits AGGMI1 on protein aggregation
I'm sending a number of these to further a study (almost complete) on the formation of pathological protein aggregates. I placed the WUs into the "short" queue - a GTX 275 (on Linux) should take around 8.5 hours for one. 17 Oct 2011 | 16:19:56 UTC · Comment

Steve Jobs' 2005 Stanford Commencement Address
A nice talk from Jobs in youtube. If you have not seen it yet, give it a try.
6 Oct 2011 | 7:27:51 UTC · Comment

Do not use BOINC 6.13.3 - 6.13.4 - 6.13.6
These (unstable and withdrawn) version are silently causing WU corruption on upload and make other WUs fail.

We encourage you to use the stable versions of BOINC clients.

Thanks 30 Sep 2011 | 22:27:08 UTC · Comment

450 WUs more to fight cancer
More WUs and counting for the Cancer-related project we are running. They come with the tag *EGFR* and are submitted to acemdlong only. Expect some 500 more in the next two weeks. Have a nice weekend. 16 Sep 2011 | 16:13:42 UTC · Comment

Simpler deadline
Since a few days, the deadline for the results is fixed at 5 days.There is not anymore any special mechanism for replication of results as before.
This change should help people with slow cards to complete workunits.

Make sure you select the right application (short 3h or long 12h) for your card.

gdf 10 Sep 2011 | 6:47:02 UTC · Comment

Welcome to Nathaniel
Nate joined our group few months ago for a phd and he has just started to submit jobs in gpugrid for all of you.

GDF 31 Aug 2011 | 16:17:38 UTC · Comment

Gpugrid in the 6th Virtual Physiological Human newsletter
The 6th public newsletter of the Virtual Physiological Human Network of Excellence includes an article about the recent scientific results obtained thanks to GPUGRID's volunteers. The article is on page 12; it features a couple of (very illustrative, in my opinion) figures which visualize the recent "TRYP" experiments. 21 Aug 2011 | 9:20:08 UTC · Comment

Updated project icon
It's just a small change (namely, 1600 pixels small) - we updated the project icon and got rid of the obsolete reference to PS3s. This is important for newer BOINC clients, whose simplified view only lists projects by icon. 19 Aug 2011 | 9:44:48 UTC · Comment

Possible network outage on 10th August
There could be a possible network outage tomorrow for network maintenance. It might affect also the new gpugrid server.

gdf 9 Aug 2011 | 19:50:11 UTC · Comment

550 "WU shots" for the Summer
Dear all,
A batch of 550 very short WUs -WU shots- (compared to GPUGRID standard) has been sent for acemd2. Tagname is *PYRT* and expected computing time is 2-3h for a GTX275. Let's see how we (you and us) like it. Happy holidays & salut! 28 Jul 2011 | 9:18:19 UTC · Comment

Crunch to fight cancer
Dear users, we are submitting several WUs (*EGF*) directly related with colorectal cancer research. We are collaborating with MDs & researchers at the Hospital del Mar here in Barcelona to characterize some previously unreported effects of a well-known drug for cancer. Thanks for your precious contribution. 27 Jul 2011 | 12:45:18 UTC · Comment

New server hardware fully funcional
We have completed the port of the server on the new hardware.

gdf, ignasi, toni 19 Jul 2011 | 18:50:41 UTC · Comment

Server up again
Please report any compute problem here.
We are still fixing some parts of the web appearance.

gdf 19 Jul 2011 | 12:41:58 UTC · Comment

Server downtime
We have a planned downtime today for a couple of hours maximum during the day.

gdf 19 Jul 2011 | 8:07:03 UTC · Comment

Server hardware update
We are checking internally the new server. Hopefully there should be a transition to the new hardware soon.

Nothing is needed on your side, but it is possible that the server can appear to be down for a couple of hours.
gdf 18 Jul 2011 | 7:23:29 UTC · Comment

New applications 6.15 are out with much improved efficiency and less impact on the system
The new applications should be both more efficient than 6.14 and eliminate any lag in the user interface in Windows.
gdf 6 Jul 2011 | 7:56:35 UTC · Comment

New batch of work KKFREE4
KKFREE4 should be fixing the problem of low credit of KKFREE3.

gdf 15 Jun 2011 | 13:43:20 UTC · Comment

New application acemdlong 6.14 is out
This new application mainly present changes in terms of the science.

gdf 12 Jun 2011 | 8:15:26 UTC · Comment

New publication in PNAS!
Dear users, we are grateful to announce a new publication from GPUGRID. This time at the prestigious journal Proceedings of the National Academy of Sciences of the USA (PNAS): http://dx.doi.org/10.1073/pnas.1103547108
The work published is related to WUs tagged as *TRYP*. Thank you very much to all contributors!
7 Jun 2011 | 7:57:01 UTC · Comment

CUDA2.2 application will be deprecated by June 3 - Update Nvidia drivers
Please update Nvidia drivers to - at least -
257.21 for Windows
256.40 for Linux
If you have a newer driver already, there is nothing to do.

gdf 28 May 2011 | 9:28:44 UTC · Comment

CUDA2.2 application will be deprecated soon - Update drivers!
Please upgrade your driver to the latest available driver. If you don't upgrade the server will not be able to send you workunits anymore as old driver are not compatible with the cuda3.1 application.

gdf 23 May 2011 | 12:46:14 UTC · Comment

(Another) New publication: optimized methods to compute binding free energies
May the party continue with our second publication from GPUGRID computations! The work, also to be published at the Journal of Chemical Theory and Computation, presents the optimization of a previously developed protocol to accurately compute binding affinities between proteins and small peptides. Such methods may be employed in the future for drug design studies. WUs related to this publication are all the *pYEEI*. Congratulations to you all!
I. Buch, S. K. Sadiq and G. De Fabritiis, Optimized potential of mean force calculations of standard binding free energy, in press J. Chem. Theory Comput. (2011) 13 May 2011 | 12:23:21 UTC · Comment

New publication: free energy of ion permeation through gramicidin A
Dears, we are happy to announce that the results of various GPUGRID-enabled studies were recently published in high-impact journals.

The first one I'd like to mention is "A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A". The paper is a numerical investigation on the convergence of a molecular dynamics (MD) technique called "steered MD" (SMD), which is used to obtain free energy profiles (i.e. probabilities of occurrence of certain biological events). The SMD technique is essentially based on statistics: one has to repeat the same experiment (computational or otherwise) over and over, many times, until a reliable result is obtained. How many times, and how reliable? Up to now, studies performed SMD on biologically-realistic systems were limited to just a few (~10) trajectories, and the corresponding error was therefore hard to assess. We used GPUGRID to perform increasing number of pulls, up to two thousands, to verify how much the precision of a free energy profile was gradually improved as a consequence. (The answer, if you were wondering, is that one needs quite a lot of simulations).

T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, in press J. Chem. Theory Comput. (2011).

Thanks to all of the crunchers of the GA* series of workunits! 10 May 2011 | 13:09:44 UTC · Comment

Social buttons and microdonations
We have added buttons for Twitter, Facebook and Flattr (social micropayments) in our website. Help us spread the project! Thanks in advance. 3 May 2011 | 10:52:22 UTC · Comment

Resuming long WU supply: ABxx
I am also resuming the supply on the long queue. They are related to amyloid proteins, involved in diseases including Alzheimer's. The new tasks took 11h on a test GTX 275.

Make sure you disable the "acemdlong" application from you GPUGRID preferences if you have an older card.

Happy Easter! 25 Apr 2011 | 15:36:03 UTC · Comment

Resuming WU supply: KKAL5
After hopefully settling the scheduler issue, I'm gradually reopening the WU faucets. I'll be sending KKAL5/6/... workunits in the standard queue, which take ~6h on a GTX275. In addition to belonging to a protein of great interest , they are also part of a new approach which hopefully makes the best use of the simulated time, re-evaluating each day (or so) the simulation threads that are more promising. (And no changes is required on your side.)

If you are not getting WUs, please post in the "server and website" forum. 22 Apr 2011 | 18:56:14 UTC · Comment

Too many workunits: Please cancel them so that other can get them
We have probably fixed the scheduler now, as there is no work, please cancel the workunits downloaded in excess so that everybody else without work can finally get them.

Many thanks,
gdf 15 Apr 2011 | 8:31:57 UTC · Comment

Problem with scheduler
In order to fix the problem that the scheduler was not releasing wus, we have switched two days ago to the matchmaker policy for the scheduler which is less strict. Well, it seems that it simply ignores all the rules, so we have now reverted to the old scheduling mechanism and will try some new fix.

gdf
15 Apr 2011 | 8:04:38 UTC · Comment

New science: AGG workunits
For some days I will be running 600 workunit chains named "AGG" in the "acemdlong" queue. They belong to an investigation on aggregation processes, e.g. those that lead to Alzheimer's disease.

13 Apr 2011 | 16:48:57 UTC · Comment

"No new work/too much work" problems
We have found what prevented most of users to receive work despite having WUs in queue. Everybody should be receiving work now. There's plenty of WUS to crunch! 13 Apr 2011 | 11:09:12 UTC · Comment

Server poweroff: Feb 24th between 7-10am (UTC +1)
Due to maintenance operations in the power system of the building, the server will be down between 7 and 10am (UTC +1) tomorrow Feb 24th. We appologise for the inconveniences. 23 Feb 2011 | 11:48:32 UTC · Comment

New task selection option
We are introducing the possibility for users to select between shorter (acemd2, approx 4 hours on GTX275 cards) and longer (acemdlong, 8 to 12 hours on GTX480) tasks. Simply go to your account preference to select which applications you want to crunch for. Long task are of course credited higher, but GPUs with less cores cannot simply compute them in time.
31 Jan 2011 | 10:06:57 UTC · Comment

Server up again
The server is up again and all should get back to normal very quickly.

gdf 27 Jan 2011 | 10:01:25 UTC · Comment

Power down scheduled: Thu, Jan 27th 10am UTC+1
The server will be down for some minutes due to power maintenace operations in the building, next Thursday January 27th at 10am (UTC+1). 21 Jan 2011 | 11:09:45 UTC · Comment

New Year, New WUs/experiment!
Happy New Year,

In this binary day 110111, I am sending some (150) new WUs tagged as *EGFR* for you to crunch. It is a brand new project that we are starting. Its goal is to find the (molecular) cause for the resistance to some anticancer drug -which is quite exciting!

More to come,
ignasi 11 Jan 2011 | 12:07:30 UTC · Comment

Happy holidays!
GPUGRID wishes you the best for the New Year. 27 Dec 2010 | 11:25:24 UTC · Comment

Long WUs are out - 50% bonus
Double sized WUs are out: *variant*_long* and include a bonus of the 50% on the credits. 14 Dec 2010 | 19:05:15 UTC · Comment

Award for conference presentation
We are glad to tell you that we received an award for best oral communication at the Young Modellers' Forum in London held the past 10th of December. The work presented was entirely based on the *IBUCH_TRYP* WUs for which the paper is in writting process. This is also your prize. Thanks for the hard work.

ignasi 14 Dec 2010 | 10:35:38 UTC · Comment

Proteins are complex molecules essential to life
Check out our University's institutional video on our research group. http://www.youtube.com/watch?v=p1TeJ61FfpI
We hope you like it. 26 Nov 2010 | 19:01:05 UTC · Comment

Network unavailable from 00:00 to 02:00 CET
There will be a planned network cut tonight from midnight to 2AM central European time zone.
There is nothing special that you need to do.
10 Nov 2010 | 9:34:52 UTC · Comment

For Fermi-CUDA3.0 users.
If you have a GTX400 series card and are using our cuda30 application, please not that we have now deprecated it and only cuda31 applications will be distributed.

To keep receiving workunits you need to update to CUDA3.1 drivers (256. or newer).

thanks,
gdf 4 Nov 2010 | 10:37:39 UTC · Comment

2,000 WUs on queue!
We are back from our WU shortage we had to impose after storage problems. Still haven't recovered from them but new light-weight WUs are out already. Come and get them! 20 Oct 2010 | 10:28:46 UTC · Comment

Storage server problem
Our 32TB storage server is offline. The sysadmins are trying to rebuild it but until then we have access to only the smaller storage. Some workunits cannot be sent.

gdf 17 Oct 2010 | 18:24:07 UTC · Comment

Server up again
We had several power cuts. The server now seems to work fine.

gdf 3 Sep 2010 | 11:05:05 UTC · Comment

Power down
Tonight we had a power down of the servers. We are still recovering from it as one disk seems to be not functional.

gdf 3 Sep 2010 | 8:40:51 UTC · Comment

On new fatty WUs
A batch of 500 WUs *_TRYP_* have been sent and will take TWICE as much to compute than normal.We are talking of 10 nanoseconds of simulation per WU! (for what most people still use big fat supercomputers). We need them for a very interesting publication we are preparing related to this experiment. Many thanks for the effort! 27 Aug 2010 | 15:23:16 UTC · Comment

Welcome back from holidays with a new publication from GPUGRID
Thanks to all volunteers for their contribution in the run of all *JAN* tasks which finally lead to this scientific publication:
J. Selent, F. Sanz, M. Pastor and G. De Fabritiis, Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors, PLOS computational biology, 6, e1000884 (2010).

Download it here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000884

In this work we show how sodium ion can modulate the activity of an important protein receptor (dopamine D2 GPCR) a drug target for the treatment of diverse central nervous system disorders (e.g. schizophrenia, Parkinson's disease). 23 Aug 2010 | 13:52:44 UTC · Comment

Free ligand binding success & continuation
Dear crunchers,
In the past months you crunched a set of WUs that aimed at observing a free ligand binding to a protein (*IBUCH_esrever*). At least 1 of the 750 simulations has reached destination! http://youtu.be/a3IsIQiEjeQ
Congratulations for this amazing result. However, we lack a bit of statistics for this event and we need to get more of these. We are extending the experiment (*IBUCH_freebind*). They're sitting in the queue, get yours! 12 Jul 2010 | 12:49:18 UTC · Comment

PhD position available to work with GPUGRID
A PhD position is available to work on
"Molecular modelling of receptor dimerisation - a physical phenomenon with high relevance for schizophrenia" at GPUGRID.
More information available at: http://multiscalelab.org/Jobs?action=AttachFile&do=view&target=PhD_position.pdf

Please distribute the PDF of the position to reach maximum audience.

gdf 6 Jul 2010 | 6:54:39 UTC · Comment

New application for CUDA3.1 is now out
A part for being faster for some workunits, it also solves the long standing bug of some older GTX260 cards.
You need a CUDA3.1 driver to download the cuda31 application.
(Windows only)
gdf 2 Jul 2010 | 20:24:12 UTC · Comment

New CUDA3.1 application for Windows now out for beta work
We have uploaded the new CUDA3.1 application for Windows. It is given only to users who accept beta work. It will be released officially in the next few days for everybody.
The CUDA3.0 application is still active for now.

gdf 30 Jun 2010 | 22:21:51 UTC · Comment

For Nvidia Fermi users - second reminder
In the next few days, we will replace the cuda3 application with a cuda3.1 application. This might not work on older drivers, so please update to the latest Nvidia drivers.

The CUDA3.0 application will be simply removed as there are many problems in the CUDA3.0 release that have been solved in CUDA3.1.

gdf 30 Jun 2010 | 16:04:17 UTC · Comment

For Nvidia Fermi users
In the next few days we will update the Fermi applications to CUDA3.1. If you have a Fermi card, please update your drivers to at least 257.21 for Windows and 256.35 for Linux. No action is required from users with other cards.

GDF 29 Jun 2010 | 7:38:03 UTC · Comment

New publication from GPUGRID
The article K. Sadiq and G. De Fabritiis,Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing, is now in press in the journal Proteins.

The work shows by means of MD simulations running on GPUGRID, several possible conformations of the HIV protease, a common target of anti-HIV drugs. In particular it was possible to release a new wide-open conformation which could present a possible useful target for new drugs.

Thanks everybody for donating their GPU computer time. The work units were called *HIV*.

A movie is also available at: Movie

A copy of the paper is available at: Paper 14 Jun 2010 | 10:49:40 UTC · Comment

Short movie for the outreach of molecular dynamics
In an effort to give the "Ultimate Explanation" of what is MD to the non-initiated, a couple of scientists (50% belonging to the GPUGRID team) made a short movie in the context of a visual storytelling course at the science park we work in. We hope you enjoy it: http://vimeo.com/12055025 8 Jun 2010 | 8:39:12 UTC · Comment

New 30% faster applications are now used for all runs
The new even faster applications are now used for all the production runs. Fermi cards are also supported for Linux and Windows by the CUDA3.0 versions.

GDF 21 May 2010 | 15:51:04 UTC · Comment

New HIV-1 protease simulations
Following recent discovery of the wide-open conformation of HIV-1 protease ( which can be found here: http://tinyurl.com/wohiv), we have sent some WUs to further investigate conformations of this enzyme. After initial testing we anticipate a large increase in the number of these WUs. 14 May 2010 | 17:01:23 UTC · Comment

Fermi application 6.73 is now out
After some beta testing the application is now available.

6 May 2010 | 9:41:14 UTC · Comment

Unboxing of our new GTX470 & 480
Here you have some shots taken this morning of the unboxing and installing of the brand new GTX470 and GTX480 donated to GPUGRID by user ftpd. Thanks so much again! http://tinyurl.com/welovefermi 23 Apr 2010 | 13:35:42 UTC · Comment

After months of waiting, Fermi arrives at GPUGRID!
We have just received the first two Fermi card (GTX480 and GTX470). We are now installing it, stay tuned for a performance update.

gdf 23 Apr 2010 | 9:57:52 UTC · Comment

New publication - RBoinc: scientists interface to DC
A new publication with the title "Distributed computing as a virtual supercomputer: tools to run and manage large-scale BOINC simulations" by GPUGRID scientists and developers Toni Giorgino, Matt Harvey and Gianni De Fabritiis, has been accepted for publication in the journal of Computer Physics Communications (DOI: 10.1016/j.cpc.2010.04.007) pdf. Scientists at GPUGRID have been using RBoinc already for a year and has proved to be a very safe and useful tool to manage work-flows in high-throughput experiments. RBoinc is already in the official BOINC source repository. 22 Apr 2010 | 12:49:53 UTC · Comment

ACEMD beta for Fermi
We have uploaded the beta application acemdbeta_*_cuda30 (for Fermi) compiled with CUDA3.0. You have to select to accept beta work in the preferences. Please help us to test it out.

gdf 30 Mar 2010 | 22:57:35 UTC · Comment

Server update
We have upgraded the server software to support Fermi cards.

GDF 30 Mar 2010 | 17:21:41 UTC · Comment

Lecture on GPUGRID results, awarded
We are proud to announce that a GPUGRID scientist was awarded the 1st Prize for oral communications after a lecture given at the 24th Molecular Modeling Workshop that took place in Erlangen (Germany) the 15-16th of March.
This tells us that science done at GPUGRID is becoming more and more relevant to the Molecular Modeling community. Congratulations to you all! http://tinyurl.com/MMWslides 19 Mar 2010 | 10:35:02 UTC · Comment

GPUGRID paper published!
We are happy to announce that the Journal of Chemical Information and Modeling has published the paper about GPUGRID. In this publication we formally introduce GPUGRID to the scientific community (technically and in terms of applications) and we show some results of the *IBUCH*pYEEI* workunits. You can read the abstract here http://tinyurl.com/gpugridpaper
Thank you very much. GPUGRID team 14 Mar 2010 | 9:10:11 UTC · Comment

More workunits available, 3,352 workunits are in the queue now
We have a backlog of 3352 workunits to be grabbed, help needed to complete them.

GPUGRID team
11 Mar 2010 | 17:55:21 UTC · Comment

GPUGRID wins a project to advance the understanding and cure of Schizophrenia
GPUGRID will be the essential computational tool in a national publicly funded project (TV3-Marato) on Schizophrenia. The aims of the project is to perform in-silico modelling of antipsychotic drug actions. One of the previous task group called *JAN* were already starting to study this problem. Thanks in advance to all volunteers and stay tuned for updates.

GDF 5 Mar 2010 | 14:35:42 UTC · Comment

Small challenge
We are doing a test of high-throughput production for a very small batch of WUs (29) named *challenge*.
If you are lucky to get one, please prioritize them over the next 24h only.

Many thanks. 25 Feb 2010 | 15:39:04 UTC · Comment

Optimizing protocols
We are already working on an optimized version of the protocol that will appear in the Journal of Chemical Information and Modelling as announced some days ago.
So far, they look very promising.

More WUs for the new application are already out! 19 Feb 2010 | 17:29:12 UTC · Comment

Science update. New journal article.
We are happy to announce that another set of scientific results was accepted today for publication. This is related to the jobs you have been running for months called *SH2*. Congratulations and thanks to everyone:

I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis, High-throughput all-atom molecular dynamics simulations using distributed computing, in press J. Chem. Inf. and Mod. (2010).

PDF

gdf 16 Feb 2010 | 21:43:37 UTC · Comment

New Nvidia application 60% faster is now out
Along side the old application, we have uploaded the new faster application for Windows (6.01) and Linux (6.02). GDF. 11 Feb 2010 | 9:22:17 UTC · Comment

Donations are back
The donations system is up and running again. 9 Feb 2010 | 10:46:39 UTC · Comment

Donations shut down temporarily
Due to a spam attack, we have shut down temporarily the donations to GPUGRID.
We will inform you when they are open again.

4 Feb 2010 | 16:20:33 UTC · Comment

Production work for beta app submitted
We have sent 1000 WUs for the new beta application.
Please note that they are actually production WUs already.
3 Feb 2010 | 17:17:51 UTC · Comment

New beta Nvidia application 60% faster.
The new Nvidia application is now out in beta. It is available by accepting beta work from GPUGRID. 3 Feb 2010 | 10:02:00 UTC · Comment

Account creation active again as usual. 31 Jan 2010 | 14:14:06 UTC · Comment

Account creation temporarily disabled
We have disable account creation temporarily. GDF 27 Jan 2010 | 23:00:00 UTC · Comment

GPUGRID wishes you a Merry Christmas
We also would like to introduce you the Xmas Donation Campaign to try to raise some funds for the project during these holidays. We are going to keep an eye over GPUGRID to make sure we don't go offline during the following days. Merry Christmas to you all and thank you very much for your support. 17 Dec 2009 | 0:00:00 UTC · Comment

MD conference impressions and GPUGRID poster for download!
As announced, GPUGRID was in the conference on MD here in Barcelona last week. We presented a poster, available for download here (Resources section), and a talk by Gianni. Both raised a lot of interest in terms of computational power available through ditributed computing and potential scientific impact of the experiments run. Best regards! 30 Nov 2009 | 0:00:00 UTC · Comment

Conference "Expanding the frontiers of molecular dynamics simulations in biology" in Barcelona next week
GPUGRID is participating to a conference concentrating the main talents in molecular dynamics in the world today. Gianni De Fabritiis will be giving a talk presenting the work on the Dopamine receptor, and Ignasi Buch will be presenting a poster (soon available in the web) on GPUGRID and the application Calculations of binding free energies (we have been recently busy with the paper! News soon). Remember to check out our gallery for pictures of the events. 19 Nov 2009 | 0:00:00 UTC · Comment

5th Pan-Galactic BOINC Workshop in Barcelona
The 5th Pan-Galactic BOINC Workshop will take place tomorrow and on Friday here in Barcelona and GPUGRID will be there. We will also be presenting a remote submission system that we use in the lab to safely interact with the server, to send/retrieve WUs from it. For more information check the wiki site http://boinc.berkeley.edu/trac/wiki/WorkShop09 21 Oct 2009 | 0:00:00 UTC · Comment

New top volunteers
Congratulation to our top volunteers. JackofAll managed to become top host, while XtremeSystems and Stoneageman keep their top volunteers and top teams position. 6 Oct 2009 | 0:00:00 UTC · Comment

Donor: Have your say, propose a research topic
GPUGRID offers the opportunity to its highest donor, once reached the target, to choose a research topic (Cancer, Alzheimer, etc.). Would you like to have your say but can't afford a high enough donation? No problem! Donations made as part of 'an interest group' (Team,...) will be considered as a unit. To donate, click here. Many thanks. 30 Sep 2009 | 0:00:00 UTC · Comment

New large batch of workunits ready to download
We have just uploaded over 4,000 new workunits. Good crunching. 28 Sep 2009 | 0:00:00 UTC · Comment

Another scientific publication on GPUGRID application ACEMD
A new publication on the ACEMD application run by GPUGRID has appeared on the Journal of Chemical Theory and Computation. M. J. Harvey and G. De Fabritiis, An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009). PDF available also at the project website. 25 Sep 2009 | 0:00:00 UTC · Comment

Windows application version updated
The Windows application has been updated. Please check your host. Driver version 185 or higher and BOINC 6.10.3 recommended. 22 Sep 2009 | 0:00:00 UTC · Comment

Linux version updated
The new Linux application is now based on CUDA2.2 and requires drivers 185.xx. 21 Sep 2009 | 0:00:00 UTC · Comment

Suggested client is now 6.10.3
If you are using Linux please update to BOINC 6.10.3. The previous suggested version 6.6.36 was not working properly on multiple GPUs. 20 Sep 2009 | 0:00:00 UTC · Comment

PayPal donations supported
We now support PayPal donations! Please follow the instructions from the donations website. Many thanks. 16 Sep 2009 | 0:00:00 UTC · Comment

Linux users: driver update
The Linux application will be updated tomorrow to CUDA2.2. Please, update to driver version 185.xx at least. 14 Sep 2009 | 0:00:00 UTC · Comment

Reminder to Linux users
Please remember to update to driver version 185.xx at least. The Linux application will be soon updated to CUDA2.2 8 Sep 2009 | 0:00:00 UTC · Comment

Top Contributors
With the aim to increase visibility of our TOP contributors, we now display permanently on our Homepage, the TOP 3 contributors by User, Host and Team. Congrats to the current ones! 7 Sep 2009 | 0:00:00 UTC · Comment

Request for donations. Get your research project, propose a target disease.
We would like to ask your help to support us with donations. In this letter we explain why and how you can participate to the biomedical research we will be able to do. 3 Sep 2009 | 0:00:00 UTC · Comment

Server disk changed
We are now back online. The server will suffer a bit of traffic for the first few hours due to all the data being transferred. 2 Sep 2009 | 0:00:00 UTC · Comment

Problems with a server disk
We are experiencing some problems with one of the server disk. We might shut down the server for small periods of time to fix the problems. 2 Sep 2009 | 0:00:00 UTC · Comment

GPUGRID distributes CUDA2.2 and CUDA2.3 applications
Since last week we are now distributing the most appropriate application version to your hardware. This will allow you to use the driver that you prefer, the most recent or an older one. 27 Aug 2009 | 0:00:00 UTC · Comment

GPUGRID gets first rank in the class
With the title 'A distributed computing system for high-throughput molecular dynamics simulations', Ignasi's masters thesis got the highest mark of the course: 9.6/10. Thank you all and let's keep on working! 25 Aug 2009 | 0:00:00 UTC · Comment

Suggested client version
The suggested BOINC client version is now 6.6.36. 20 Aug 2009 | 0:00:00 UTC · Comment

Windows application updated to CUDA2.2
We have updated the Windows application (version 6.67) to cuda2.2 31 Jul 2009 | 0:00:00 UTC · Comment

Server software updated
We have updated to the latest server software. 28 Jul 2009 | 0:00:00 UTC · Comment

Updating driver for LINUX users
Linux users can now update to the latest version of Nvidia drivers. We have hacked the BOINC-driver bug. Version 185.xx will be required in the future to be compatible with CUDA2.2. 27 Jul 2009 | 0:00:00 UTC · Comment

Updating driver for Windows users
The driver required will be at least 185.xx, that is required for CUDA2.2. If 190.xx works for you, you can also install it. 25 Jul 2009 | 0:00:00 UTC · Comment

Updating driver for Windows users
All Windows users should update their Nvidia driver to version 190.xx. This driver allows computation also in SLI mode. From next week, we will update the application to CUDA2.2 which requires the new driver. The current application for Windows will still work under the new driver in the meanwhile. 25 Jul 2009 | 0:00:00 UTC · Comment

Computing preferences updated
We have updated the 'computing preferences' page available under your user account in the website. Please, make sure they match your favourite computing setup. 20 Jul 2009 | 0:00:00 UTC · Comment

GPUGRID fatured in the latest VPH project newsletter
A 'technical report' on GPUGRID project is featured in the latest newsletter of the Virtual Physiological Human Network of Excellence (VPH NoE). The VPH is a large collaborative project that coordinates the efforts of the best European research institutes which work on the simulation of various aspects of the human body. See http://tinyurl.com/vph-newsletter-pdf (we are on pages 13 and 20) 15 Jul 2009 | 0:00:00 UTC · Comment

Thousands of WUs
It seems that we had some transitory issues with the scheduler, and no WUs were sent. Right now it is working fine. There are thousands of WUs waiting for you, come and get yours! 9 Jul 2009 | 0:00:00 UTC · Comment

Freed server disk space
Tonight (Mediterranean time) we ran out of disk space in the server, so most of you couldn't upload any WU. We optimized (once again) the disk space and are back normality now. Sorry for the inconveniences. 8 Jul 2009 | 0:00:00 UTC · Comment

2 billion credits reached!
The GPUGRID.net project just awarded its 2 billionth credit! This means that in totat you donated around a sextillion (10^21) floating point operations, which we used to compute approximately 1 millisecond of simulated trajectories in total. Congratulations to all volunteers! 23 Jun 2009 | 0:00:00 UTC · Comment

Server update
We have updated to the latest server software. Also now the minimum required driver version is enforced to be at least 180. 19 Jun 2009 | 0:00:00 UTC · Comment

Big queue of fresh WU!
We have +2,000 WU in queue to be crunched waiting for you guys! Actually, and that's for real, the publication on the SH2 system may be able to drop off finally after these results. Not only these, but Ignasi is defending his Masters thesis this Friday and would be delighted to show these results (properly credited of course). Many thanks in advance! 15 Jun 2009 | 0:00:00 UTC · Comment

The VPH project featured in 'The Times'
The VPH project, in which GPUGRID participates, has been in the news. 'The Times' reported today that the use of animal experiments could be replaced by research on "virtual human beings" and tests on banks of living cells within a generation, following a series of talks given at the Cheltenham Science Festival on June 4th 2009. More information here. 5 Jun 2009 | 0:00:00 UTC · Comment

New scientific paper on ACEMD, the MD compute engine of GPUGRID.net
We are glad to announce the publication of our application, ACEMD, in the Journal of Chemical Theory and Computation. For more information: Journal link and pdf. 28 May 2009 | 0:00:00 UTC · Comment

GPUGRID in the Virtual Physiological Human project
GPUGRID participates to the VPH-NoE (www.vph-noe.eu), the EU-supported Network of Excellence for the Virtual Physiological Human. The VPH NoE initiative supports European research in biomedical modelling and simulation of the human body. It will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare. For more information check the VPH official site 26 May 2009 | 0:00:00 UTC · Comment

WUs, WUs and more WUs
We've recently sent hundreds of new batches of workunits. There's a long queue of them waiting to be downloaded. Come and get yours! 22 May 2009 | 0:00:00 UTC · Comment

GPUGRID featured in latest EMBO Report
The GPUGRID project is featured in "Science wikinomics", a paper in the latest EMBO (European Molecular Biology Organization) Reports, which discusses the philosophy of distributed scientific computing in the "wiki" scientific workplace. Article link 13 May 2009 | 0:00:00 UTC · Comment

Donate to GPUGRID
GPUGRID is now accepting donations from users who want to contribute further. We do accept either hardware or monetary donations. Monetary donations have a minimum of 1 Euro and can be done using a Credit/Debit card or via Bank Transfer. Many thanks to all of you considering a donation. 7 May 2009 | 0:00:00 UTC · Comment

On recent WU cancellations and redundancies
Yesterday we had to cancel several WU due to an emergency related to inherited problems from Easter's blackout and our efforts to improve our in-house developed submission system. In addition, the fact that the output of such cancellations wasthe same to that the 'redundant results' lead to some confusion between these two states. The GPUGRID team appologizes for any credit lost in the case of the emergency cancellations but reminds again its users that NO CREDIT NEITHER COMPUTING TIME is lost in the case of common redundancy in results. We refer to this post and [url=http://www.gpugrid.net/forum_thread.php?id=868&nowr ap=true#7762]this one[/url] for information information. Thank you very much for your patience. 28 Apr 2009 | 0:00:00 UTC · Comment

New WUs are out - An HIV virus (AIDS) protein
So we are submitting new WUs corresponding to a brand new experiment. We are starting to investigate the structural and dynamical properties of HIV viral proteins in order to help understand how at a molecular level, the virus becomes infectious. We will soon update the science section for it. 24 Apr 2009 | 0:00:00 UTC · Comment

GPUGRID server is up and running again
We suffered a network failure during these Easter holidays that couldn't be fixed until today. We are getting back to normality now. Thanks for your patience. 14 Apr 2009 | 0:00:00 UTC · Comment

Heartquake in Abruzzo
Da GPUGRID vogliamo esprimere la nostra piu' sincera partecipazione a questo triste giorno di lutto nazionale in Italia per le vittime del terremoto. GDF. (http://www.repubblica.it) 10 Apr 2009 | 0:00:00 UTC · Comment

A new batch of workunits out
We have just submitted a new batch of workunits which improve further the accuracy of the free energy calculations. 3 Apr 2009 | 0:00:00 UTC · Comment

We are billionaires
We just reached a 1 billion (1,000,000,000) total credits! Many thanks to all volunteers. 27 Mar 2009 | 0:00:00 UTC · Comment

Spring upload
More New WUs are out! We didn't want you to start spring with no new stuff to crunch. Have a nice weekend! 20 Mar 2009 | 0:00:00 UTC · Comment

New workunits are out
We are giving away new workunits for the SH2 system (see Science page for more info). These are similar simulations but with different ligands as the computing protocol we've been applying for the last months seems to do pretty well. We are very excited about it. Thanks to all who make it possible! 18 Mar 2009 | 0:00:00 UTC · Comment

Server update and HTTP error fixes
We have updated the server software. The problems of HTTP errors have been solved as well. 12 Mar 2009 | 0:00:00 UTC · Comment

New GPU applications
New applications for Windows and Linux released. CPU usage is now close to zero, so that you can keep crunching other CPU projects as before while also using the GPUs in your machine. 30 Jan 2009 | 0:00:00 UTC · Comment

NVIDIA Press Release
GPU computing finally takes off in BOINC with GPUGRID, SETI@Home and Einstein@Home. Read today's NVIDIA press release 'NVIDIA CUDA Technology Dramatically Advances The Pace Of Scientific Research'. 17 Dec 2008 | 0:00:00 UTC · Comment

Suggested BOINC version is now 6.4.5
Please upgrade to version 6.4.5 to have a correct estimation of elapsed time. 11 Dec 2008 | 0:00:00 UTC · Comment

GPUGRID t-shirt graphics and brochures available from website.
We have created a new resource section which contains project brochures and t-shirt graphics and divulgation material. 27 Nov 2008 | 0:00:00 UTC · Comment

PS3GRID and GPUGRID new website in two styles selectable by users.
We have uploaded the new website with improved design and usability. Users can also choose between black (geek) and white (zen) styles. Try it out. 12 Nov 2008 | 0:00:00 UTC · Comment

GPUGRID - BOINC version 6.3.19
BOINC release 6.3.19 is now the suggested version for GPU users. Please update following the link from www.gpugrid.net. 29 Oct 2008 | 0:00:00 UTC · Comment

GPUGRID video and photo channels
The multiscalelab is pleased to announce its new video channel on vimeo: http://www.vimeo.com/user862246. We have uploaded a sample video of a simulation (more news soon) and a screencast on how to connect a GPU to the project using Vista. We want to remind as well, that we are already present on flickr: http://www.flickr.com/photos/multiscalelab 24 Oct 2008 | 0:00:00 UTC · Comment

GPUGRID new applications
The new application for Linux and Windows are now 25% faster on GTX200 Nvidia cards. We are now officially supporting Windows 32 and 64, XP and Vista. 20 Oct 2008 | 0:00:00 UTC · Comment

Play Me a Molecule, PS3GRID/GPUGRID note on Science magazine
A note featuring PS3GRID/GPUGRID has appeared on the September 12 issue of Science. Thanks to all volunteers for their contribution to the continuos growth of this project. Full text is at http://www.sciencemag.org/cgi/content/long/321/5895/1425b 29 Sep 2008 | 0:00:00 UTC · Comment

GPUGRID new application
We have uploaded a new GPU application version for Linux with practically zero CPU usage. 12 Sep 2008 | 0:00:00 UTC · Comment

PS3GRID-GPUGRID milestone 1,000,000 RAC per day
In the past few days PS3GRID-GPUGRID project reached and passed the 1,000,000 RAC per day. A computational milestone for the project ever reached before. 6 Sep 2008 | 0:00:00 UTC · Comment

Server are up and running
We had a network outage during Sunday due to electrical works. All normal now. 26 Aug 2008 | 0:00:00 UTC · Comment

GPU new applications
We have uploaded new applications compatible with CUDA 2.0 and latest Nvidia drivers (177.xx). Please reset project in order to get the right latest files. 26 Aug 2008 | 0:00:00 UTC · Comment

GPU BOINC update
ALL LINUX users of the GPU application should update to boinc version 6.3.8. Link available from www.gpugrid.net. 20 Aug 2008 | 0:00:00 UTC · Comment

New article in press
The impact of accelerator processors for high-throughput molecular modeling and simulation, in press Drug Discovery Today (2008). 5 Aug 2008 | 0:00:00 UTC · Comment

Launch of GPUGRID.net, BOINC on GPUs
Finally GPU computing on BOINC! After delivering BOINC on Playstation last year, we are happy to announce that from today we are are able to distribute workunits on Nvidia GPUs. PS3grid.net and the new website GPUGRID.net go along to create a large infrastructure for biomolecular simulations. To run GPU workunits simply follow the instructions on the website. Apart from us, this was made possible by a strong collaboration with BOINC developers and in particular David Anderson at Berkeley and Stefan and Keith from the BOINC community, already moderators at ps3grid. We also want to thank Nvidia for their important support. 17 Jul 2008 | 0:00:00 UTC · Comment

PS3GRID at the European Science Open Forum
Come and visit us at our booth at the ESOF08 event taking place in Barcelona this Friday. http://www.esof2008.org. 17 Jul 2008 | 0:00:00 UTC · Comment

Sony Computer Entertainment Spain collaborates with PS3GRID
PS3GRID announces a collaboration with Sony Computer Entertainment Spain which donated to the project 20 Playstation3 to build a PS3 cluster and funds to support a Master student project. The PS3 cluster will be presented at the European Science Open Forum, 18 July 2008 in Barcelona, http://www.esof2008.org. Photos of the cluster and the PS3GRID showcase will be made available after the event. 9 Jul 2008 | 0:00:00 UTC · Comment

Server update.
PS3GRID updated to the lastest server release. 21 May 2008 | 0:00:00 UTC · Comment

Detail of the first numerical experiment.
The first set of numerical experiments run on ps3grid.net produced 5,000 trajectories, 4 microseconds of simulated time, over 200 years of CPU time with a daily output of 100 ns and few GBytes, two orders of magnitude closer to single-molecule pulling experiments. Thanks to all volunteers for this effort. 9 May 2008 | 0:00:00 UTC · Comment

Forums update.
PS3GRID forums have been slightly reorganized to improve the usability. 10 Apr 2008 | 0:00:00 UTC · Comment

Server is up.
Server is up again after PRBB server room maintainance. 31 Mar 2008 | 0:00:00 UTC · Comment

Master URL change for www.ps3grid.net.
The master url of the project has changed to the simpler http://www.ps3grid.net. Previous master url will still work, although the boinc client will notify that you should use the new one. 28 Mar 2008 | 0:00:00 UTC · Comment

Server downtime tomorrow March 28.
Tomorrow Friday, there will be a general shutdown in the PRBB server room which will affect ps3grid.net. The server will remain down for approximatevely 4 hours. Everything should get back to normal after the server is booted again. 27 Mar 2008 | 0:00:00 UTC · Comment

Boinc.cat and ps3grid.net on the press.
An article featuring boinc.cat and ps3grid has just appeared in a Spanish newspaper. 3 Mar 2008 | 0:00:00 UTC · Comment

New numerical experiment on TPI.
We have released a new batch of workunits for a second set of molecular experiments. 26 Feb 2008 | 0:00:00 UTC · Comment

New PS3GRID live pen drive released.
We have released an updated version of the ps3grid live pendrive compatible with firmware version 2.10. 11 Feb 2008 | 0:00:00 UTC · Comment

PS3GRID server storage upgrade.
We are upgrading the disk space on the ps3grid server. It might be down for short periods today. 7 Feb 2008 | 0:00:00 UTC · Comment

PS3GRID user photo.
We are looking for photos of PS3GRID users with their PS3(s) for a Spanish national magazine. If you wish to appear follow this thread in the forum . 1 Feb 2008 | 0:00:00 UTC · Comment

PS3GRID server update.
PS3GRID may be down at times today for a server update. 22 Jan 2008 | 0:00:00 UTC · Comment

PS3GRID new server.
PS3GRID new server is now in place. Everything seemed to have worked smoothly. 14 Dec 2007 | 0:00:00 UTC · Comment

PS3GRID new server.
PS3GRID moved to the new server. The server will remain mostly down for tests until Dec 14 at 1PM, Barcelona. 14 Dec 2007 | 0:00:00 UTC · Comment

PS3GRID new server.
PS3GRID will move to a new server. The move will take place between today and tomorrow. During the DNS propagation the server may appear unreachable from your location. 13 Dec 2007 | 0:00:00 UTC · Comment

PS3GRID Live on LaVanguardia.
PS3GRID Live usb reported in the Catalan newspaper LaVanguardia. 3 Dec 2007 | 0:00:00 UTC · Comment

PS3GRID Live download stats.
PS3GRID Live usb has been downloaded 115 times in just 5 days. 19 Nov 2007 | 0:00:00 UTC · Comment

PS3GRID Live Linux pen drive simplifies volunteer computing on the Playstation 3.
PS3GRID has just relased a new usb pen drive image called PS3GRID live to start BOINC/Linux within minutes on a PlayStation 3. 14 Nov 2007 | 0:00:00 UTC · Comment

Network problems.
University network returned to normal acitivity. 10 Nov 2007 | 0:00:00 UTC · Comment

PS3GRID project update.
PS3GRID project has been updated to the latest BOINC version. 10 Nov 2007 | 0:00:00 UTC · Comment

PS3GRID project is up. 4 Nov 2007 | 0:00:00 UTC · Comment

New client for IBM CELL blades at PS3GRID.NET
A new version of the PS3GRID BOINC client is available for download. This version has better support for IBM CELL blades. Playstation 3 users do not need to upgrade. 30 Oct 2007 | 0:00:00 UTC · Comment

Research jobs at PS3GRID.NET
PhD studentiship at PS3GRID.NET: Medium-throughput Modelling of Protein-Ligand Interactions Using Distributed Computing 22 Oct 2007 | 0:00:00 UTC · Comment

Read about PS3GRID.NET in this new document uploaded on PS3GRID.NET. 20 Oct 2007 | 0:00:00 UTC · Comment

PS3 price cut in Europe from 10th Oct
A 40Gb PS3 version will be available from next month in Europe and elsewhere (not north America) at a discounted price. Read more 8 Oct 2007 | 0:00:00 UTC · Comment

D. Anderson gives a seminar at the PRBB.
Next Monday September 10 at 12:00 seminar Volunteer Computing in Biomedicine by D. Anderson, at the Barcelona Biomedical Research Park. All welcome. 3 Sep 2007 | 0:00:00 UTC · Comment

PS3GRID on SuperQuark.
The Barcelona Biomedical Research Park and PS3GRID featured on the national Italian television. Click here to watch (in Italian). 28 Aug 2007 | 0:00:00 UTC · Comment

PS3GRID publication.
A chapter on PS3GRID will appear in the book 'Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities'. 22 Aug 2007 | 0:00:00 UTC · Comment

PS3GRID web site translations.
Many thanks to toma01 for the Japanese translation and to Miquel P. for the Catalan and Spanish ones. 13 Aug 2007 | 0:00:00 UTC · Comment

Work available.
A new large batch of workunits is available. The first set of new work is already out. 1 Aug 2007 | 0:00:00 UTC · Comment

Translation.
PS3GRID website is now also available in Spanish and Japanese. Other translations to follow. 23 Jul 2007 | 0:00:00 UTC · Comment

D. Anderson gives a seminar at the PRBB.
Seminar title Volunteer Computing in Biomedicine by D. Anderson, September 10 at 12:00 at the Barcelona Biomedical Research Park. All welcome. 18 Jul 2007 | 0:00:00 UTC · Comment

Website and server running.
We are online now. The problem occurred is fixed and will be solved completely in the next days. 16 Jul 2007 | 0:00:00 UTC · Comment

Database problems.
We are experiencing problems with the database due to an other webserver hosted on the server. Unlikely that we can fix it before Monday. 14 Jul 2007 | 0:00:00 UTC · Comment

PS3GRID Boinc Client.
A new release of the PlayStation 3 BOINC client with an easier installation and execution script is now downloadable from PS3GRID. 12 Jul 2007 | 0:00:00 UTC · Comment

Price cut for PS3.
In USA Sony cuts PlayStation3 price by 100 dollars. Hopefully the same will happen in Europe. 9 Jul 2007 | 0:00:00 UTC · Comment

New website.
PS3GRID has a new website professionally designed by mantis.cat. Many thanks to them and Dani. 6 Jul 2007 | 0:00:00 UTC · Comment

Public presentation.
The first results computed for the PS3GRID project will be presented at the international symposium of biomedical informatics, 26-27 June Barcelona. 24 Jun 2007 | 0:00:00 UTC · Comment

Server upgrade.
Today server will be down at times for software upgrade. 19 Jun 2007 | 0:00:00 UTC · Comment

Translation update.
PS3GRID volunteers are translating the website in French, German, Italian, Spanish, Catalan, Portuguese and Japanese. 16 Jun 2007 | 0:00:00 UTC · Comment

Favicon.
Thanks to Krunchin-Keith for the new PS3GRID favicon and congratulations for the top user ranking. 13 Jun 2007 | 0:00:00 UTC · Comment

Workunits.
New work is now available. 13 Jun 2007 | 0:00:00 UTC · Comment

Congratulations.
Beta Users have successfully created over 50 molecular trajectories for something equivalent to over 632 days (1.7 years) of CPU-time on a PC. 11 Jun 2007 | 0:00:00 UTC · Comment

Translations.
We are looking for translators in French, German, Italian, Japanese and other major languages. Please contact ps3grid@gmail.com if you wish to help. 8 Jun 2007 | 0:00:00 UTC · Comment

Project skin.
Project skin images are now showing in the client. Thanks to Dani at boinc.cat. 5 Jun 2007 | 0:00:00 UTC · Comment

Beta testing.
Further workunits are available. 29 May 2007 | 0:00:00 UTC · Comment

Beta testing.
First workunits for 1875 credits are being distributed. 26 May 2007 | 0:00:00 UTC · Comment

Beta testing.
PS3GRID enters BETA testing phase. If you own a PlayStation3 and wish to participate, please write to ps3grid@gmail.com 12 May 2007 | 0:00:00 UTC · Comment

AVUI (Catalan)
An article on the journal Avui on BOINC and ps3grid 9 May 2007 | 0:00:00 UTC · Comment

Innovation (French)
Article on the journal Innovation on ps3grid 4 May 2007 | 0:00:00 UTC · Comment

Tv3 News (by Dani) (Catalan/Spanish)
Watch the news program on the ps3grid project on TV3 3 May 2007 | 0:00:00 UTC · Comment

Radio interview at comradio (by Dani) (Spanish, 12min, 6Mb)
Listen to the interview of G. De Fabritiis on the use of the Cell processor for scientific computing. 25 Apr 2007 | 0:00:00 UTC · Comment

Beta testing on PS3GRID will be starting in a couple of weeks 23 Apr 2007 | 0:00:00 UTC · Comment

G. De Fabritiis
Performance of the Cell processor for biomolecular simulations 2 Mar 2007 | 0:00:00 UTC · Comment

Vilaweb
PlayStation3 serving scientists -Catalan press- 13 Feb 2007 | 0:00:00 UTC · Comment

El Mundo
Potential of the PlayStation 3 for scientist projects development -Spanish press- 10 Feb 2007 | 0:00:00 UTC · Comment

El Mundo Salud
Potential of the PlayStation 3 for scientist projects development (on-line version) -Spanish press- 10 Feb 2007 | 0:00:00 UTC · Comment

Hello World
PS3GRID.NET started its website 1 Feb 2007 | 0:00:00 UTC · Comment

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