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

SGER：CHARMM 的副本交换 STMD：生物物理计算领域的潜在重大进步

• 批准号: 0833605
• 负责人: Thomas Keyes
• 金额: $ 13.5万
• 依托单位: Trustees of Boston University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2012-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0833605&HistoricalAwards=false
• 关键词: SGER; Replica; Exchange; STMD; CHARMM

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.

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。波士顿大学的托马斯凯斯是由理论和计算化学计划的SGER奖支持，以提供最广泛使用的生物模拟应用程序，CHARMM，具有使用复制交换统计温度分子动力学，RESTMD的能力。STMD算法及其对副本交换的扩展是在NSF-ITR资助下开发的，在相对简单的系统上，在所有测试中都大大优于竞争对手的增强型采样算法。 凯斯和他的研究小组正在探索同样的优势适用于生物物理化学中最具挑战性问题的现实模拟的可能性，其中对热重要状态的准确采样至关重要，而且很困难。RESTMD+CHARMM计划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（包括健康相关病毒、蛋白质错误折叠和聚集）的准确采样成为可能。它将免费提供给所有CHARMM用户。