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Molecular dynamics (MD) is a simulation methodology which enables, for instance, the study of the dynamics of proteins in their environment. It is used in academia and by pharma companies for a wide variety of applications, including drug design, drug screening and in general to investigate protein function.
Each atom is represented using classical equations of motion (Netwon's equation) and evolves according to a force field which models the chemical nature of each atom (Carbon, Oxygen, Hydrogen and so on) in its local environment. In principle each atom interacts with all the others within a certain interaction radius, as, at long distances, the interaction between atoms is weaker (usually between 10 to 12 A (Angstrom is 1E-10 meters). Each step of a molecular dynamics code usually corresponds to just 1 fs (10E-15 seconds). Both factors contribute to the large computational cost of molecular dynamics simulations: bridging molecular, atomistic scales (of the order of nanosecond) with biological scales (micro-milli seconds) is therefore a big challenge in computational biology. If we manage to overcome this limitation, then biomedical applications of molecular dynamics are limitless.
In full-atom molecular dynamics simulations proteins, lipid membrane, water molecules, ions, and so on are represented by all their atoms. This is the most common molecular dynamics simulation performed by scientists but also the most expensive. The advantage that all the molecular specificity of the system is taken into account (for instance the water around the protein is often very important) but the computing cost is so big that often simulations can be run only on large and expensive supercomputers. Indeed, often these simulations use tens to hundreds of processors.
PS3GRID, the Cell processor and PlayStation3 make suddenly possible to run full atom molecular dynamics on a single PS3 with a good return time. The large number of PS3s available makes possible to use different computational protocols to exploit parallel independent runs and compute the energetics of the system (a fundamental thermodynamic quantity to understand the system).
PS3GRID users are running entire molecular systems representing part of a cell membrane for instance with over 30,000 to 100,000 atoms depending on the problem. The results collected from several runs are analyzed. In this sense, PS3GRID is not a single application or single problem project, rather it is a novel computational tool made available to computational scientists. We are in fact collaborating with other academic research group. Each new application will be described on the website and the scientific outcome reported.
