Macromolecular Modeling

National Institute Of Environmental Health Sciences

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Abstract

During this fiscal year we devoted considerable efforts towards efficient highly parallel implementations of classical molecular dynamics. The highly efficient PMEMD molecular dynamics code developed and maintained by our group (in particular Bob Duke) was further developed to achieve parallel scaling out to hundreds of processors, allowing us to thoroughly simulate the large protein complexes involved in blood coagulation and related processes. We also explored and modified two recent accelerated sampling methodologies, allowing thorough exploration of conformational free energy surfaces. Importantly, these new methods open new possibilities beyond the reach of conventional molecular simulations.