NAMD: The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field. ALCF-2 Early Science Program Technical Report.

摘要

Large-scale Molecular dynamics (MD) simulation based on atomic models provide a powerful tool to understand the structure-dynamics-function relationships of important biological systems. Recent advances in computing power, especially in supercomputer, make MD simulation more and more popular in modern scientific community. However, the power of classical MD simulation has been limited mainly by the accuracy of the potential energy function and the efficiency of the dynamic algorithm enabling the adequate configurational sampling. This Early Science Project is aimed to make MD simulation method go beyond current limit using the leadership supercomputer Blue Gene/Q Mira. To address the issue of potential energy accuracy, classical Drude oscillator is developed to take into account the electronic polarizability in molecular systems. In order to develop and test the Drude polarizable force field for biomolecules, extensive MD simulations of typical polypeptides, lipids are needed. This requires efficient dynamic sampling algorithm that allows fast sampling. The sampling issue can be addressed by using advanced strategies based on multiple copies in order to enhance the sampling efficiency of brute-force MD. One such method is called replica-exchange MD (REMD).