Hamiltonian replica-exchange in GROMACS: a flexible implementation
Computational Physics
2014-09-30 v1 Statistical Mechanics
Biological Physics
Chemical Physics
Abstract
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.
Cite
@article{arxiv.1307.5144,
title = {Hamiltonian replica-exchange in GROMACS: a flexible implementation},
author = {Giovanni Bussi},
journal= {arXiv preprint arXiv:1307.5144},
year = {2014}
}
Comments
To appear on Molecular Physics