SGER: Replica Exchange STMD for CHARMM: a Potentially Large Advance in Biophysical Computing

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。波士顿大学的Thomas Keyes得到了理论和计算化学项目SGER奖的支持，提供了最广泛使用的生物模拟应用CHARMM，具有使用复制交换统计温度分子动力学RESTMD的能力。STMD算法及其扩展到副本交换是在NSF-ITR资助下开发的，并且在相对简单的系统上的所有测试中都大大优于竞争的增强采样算法。Keyes和他的研究小组正在探索同样的优势在生物物理化学中最具挑战性的问题的现实模拟中的可能性，在这些问题中，热重要状态的精确采样是至关重要的，也是困难的。RESTMD+CHARMM项目对生物物理模拟具有潜在的巨大影响，使目前难以处理的大型复杂系统（包括与健康相关的病毒、蛋白质错误折叠和聚集）的精确采样成为可能。它将免费提供给所有CHARMM用户。

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).Thomas Keyes of Boston University is supported by a SGER award from the Theoretical and Computational Chemistry program to provide the most widely used biosimulation application, CHARMM, with the capability to use replica exchange statistical temperature molecular dynamics, RESTMD. The STMD algorithm, and its extension to replica exchange, were developed under an NSF-ITR grant, and have substantially outperformed competing enhanced sampling algorithms in all tests, on relatively simple systems. Keyes and his research group are exploring the possibility that the same advantages hold for realistic simulations of the most challenging problems in biophysical chemistry, where accurate sampling of the thermally important states is crucial, and difficult. The RESTMD+CHARMM program has a potentially large impact on biophysical simulation, making possible accurate sampling of large, complex systems that are currently intractable, including health related viruses, and protein misfolding and aggregation. It will be freely available to all CHARMM users.