A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations
收藏doi.org2025-01-22 收录
下载链接：
http://doi.org/10.17632/yk73j46v4b.1
下载链接
链接失效反馈官方服务：
资源简介：
Abstract
Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters co...
Title of program: REST2-NAMD
Catalogue Id: AEXX_v1_0
Nature of problem
A generic implementation providing user-friendly API including input file preparation and performing replica exchange, and high frequency exchange attempt frequency with minimal communication overhead.
Versions of this program held in the CPC repository in Mendeley Data
AEXX_v1_0; REST2-NAMD; 10.1016/j.cpc.2015.08.030
This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
摘要
REST2（溶液退火复制品交换）是一种强大的分子动力学（MD）采样增强算法，其在显著减少复制品数量的同时，相较于标准的温度交换算法，实现了更高的采样效率。在本研究中，我们通过在高度可扩展的MD软件NAMD中实现一种稳健且通用的方法，扩展了REST2在定量生物物理模拟中的应用。力场参数的缩放程序...
提供机构：
Mendeley Data
