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.

To appear on Molecular Physics

References in corpus (3)

• Canonical sampling through velocity-rescaling
• Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
• PLUMED: a portable plugin for free-energy calculations with molecular dynamics

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