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.

Hamiltonian replica-exchange in GROMACS: a flexible implementation / Bussi, G.. - In: MOLECULAR PHYSICS. - ISSN 0026-8976. - 112:3-4(2014), pp. 379-384. [10.1080/00268976.2013.824126]

Hamiltonian replica-exchange in GROMACS: a flexible implementation

Bussi, G.
2014-01-01

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.
2014
112
3-4
379
384
10.1080/00268976.2013.824126
https://arxiv.org/abs/1307.5144
Bussi, G.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/15840
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