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.| File | Dimensione | Formato | |
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