Hamiltonian replica exchange in GROMACS: a flexible implementation
Hamiltonian replica exchange in GROMACS: a flexible implementation
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DOI：
10.1080/00268976.2013.824126
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发表时间：
2014-02-16
影响因子：
1.7
通讯作者：
Bussi, Giovanni
中科院分区：
文献类型：
--
作者：
Bussi, Giovanni
介绍了一种在分子动力学软件GROMACS中实现哈密顿副本交换的简单通用方法。在该实现中，任意不同的哈密尔顿算子可以用于不同的副本，而不会导致任何显著的性能损失。该实现在一个简单的玩具模型上进行了验证-丙氨酸二肽在水中-并应用于研究RNA四环的重排，在那里它被用来比较最近提出的力场校正。
A simple and general implementation of Hamiltonian replica exchange for the popular molecular dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections.