1307.5144 (Giovanni Bussi)

Hamiltonian replica-exchange in GROMACS: a flexible implementation    [PDF]

Giovanni Bussi

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.

View original: http://arxiv.org/abs/1307.5144