An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Abstract Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulation... Title of program: TIGER2-NAMD Catalogue Id: AEWC_v1_0 Nature of problem Replica Exchange Molecular Dynamics Versions of this program held in the CPC repository in Mendeley Data AEWC_v1_0; TIGER2-NAMD; 10.1016/j.cpc.2015.02.025 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)摘要 本文提出了一种改进的TIGER2副本交换分子动力学（Replica Exchange Molecular Dynamics，REMD）方法的实现方案，采用当代版本NAMD分子动力学软件包内置的副本交换应用程序编程接口（Application Programming Interface，API）。该实现以TCL脚本的形式呈现，可与标准配置文件配合使用。本实现通过与此前的TIGER2实现方案以及已报道的原始TIGER2模拟数据进行对比验证…… 程序名称：TIGER2-NAMD 目录编号：AEWC_v1_0 问题属性：副本交换分子动力学 Mendeley数据平台CPC文库中收录的本程序版本： AEWC_v1_0; TIGER2-NAMD; 10.1016/j.cpc.2015.02.025 本程序源自贝尔法斯特女王大学馆藏的CPC程序库（1969-2018）