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

该奖项由2009年《美国复苏和再投资法案》(Public Law 111-5)资助。波士顿大学的Thomas Kyes获得了理论和计算化学项目颁发的SGER奖的支持，该奖项旨在提供使用最广泛的生物模拟应用程序CHARMM，该应用程序能够使用副本交换统计温度分子动力学RESTMD。STMD算法及其对副本交换的扩展是在NSF-ITR拨款下开发的，在相对简单的系统上的所有测试中都大大超过了竞争的增强型采样算法。凯斯和他的研究小组正在探索这样一种可能性，即同样的优势也适用于生物物理化学中最具挑战性的问题的现实模拟，在生物物理化学中，对热重要状态的准确采样是至关重要的，也是困难的。RESTMD+CHARMM计划对生物物理模拟有潜在的巨大影响，使目前难以处理的大型复杂系统的准确采样成为可能，包括与健康相关的病毒，以及蛋白质的错误折叠和聚集。它将向所有CHARMM用户免费提供。

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.