Hamiltonian replica-exchange in GROMACS: a flexible implementation

TL;DR

This paper introduces a flexible Hamiltonian replica exchange implementation in GROMACS that allows different Hamiltonians for replicas without performance loss, validated on a toy model and applied to RNA tetraloop studies.

Contribution

It presents a general, efficient implementation of Hamiltonian replica exchange in GROMACS supporting diverse Hamiltonians for enhanced molecular simulations.

Findings

Validated on alanine dipeptide in water

Applied to RNA tetraloop rearrangement

Compared force-field corrections effectively

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.