Hamiltonian replica exchange in GROMACS: A flexible implementation

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. © 2013 Taylor & Francis.