Hamiltonian replica exchange in GROMACS: a flexible implementation

被引：186

作者：

Bussi, Giovanni ^{[1
]}

机构：

[1] SISSA, I-34014 Trieste, Italy

来源：

MOLECULAR PHYSICS | 2014年 / 112卷 / 3-4期

基金：

欧洲研究理事会;

关键词：

Hamiltonian replica exchange; solute tempering; RNA tetraloop; PARTICLE MESH EWALD; SMALL RNA HAIRPIN; MOLECULAR-DYNAMICS; FORCE-FIELD; BIOMOLECULAR SYSTEMS; ENERGY LANDSCAPE; NUCLEIC-ACIDS; SIMULATIONS; ALGORITHM; EFFICIENT;

D O I：

10.1080/00268976.2013.824126

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

收藏

页码：379 / 384

页数：6

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