Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
复制标题
DOI：
10.1016/j.cplett.2003.12.039
复制
发表时间：
2004-01-26
影响因子：
2.8
通讯作者：
Brandsdal, BO
中科院分区：
文献类型：
--
作者：
Åqvist, J;Wennerström, P;Brandsdal, BO
研究了分子动力学/蒙特卡罗（MD/MC）混合算法对任意分子体系的定压模拟。计算报告在环境和高压下的液态水系统和溶剂化酶的化学反应步骤，利用经验价键势。本方法再现较早报道的结果以及计算效率，因为它不需要维里进行评估，在每个MD步骤。研究还发现，只要适当选择体积步长和更新频率，引入MC体积步长对系统动力学特性的影响可以忽略不计。(C)2003 Elsevier B. V.保留所有权利。
A mixed molecular dynamics/Monte Carlo (MD/MC) algorithm for constant pressure simulations of arbitrary molecular systems is examined. Calculations are reported at ambient and high pressures both for liquid water systems and for a chemical reaction step in a solvated enzyme utilizing empirical valence bond potentials. The present method reproduces earlier reported results well and is computationally efficient since it does not require the virial to be evaluated at each MD step. It is also found that the effects of introducing MC volume steps on the dynamics of the system are negligible provided that the volume step sizes and updating frequencies are appropriately chosen. (C) 2003 Elsevier B.V. All rights reserved.