w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations | Zendy

Mehrnoosh Arrar | Zendy; César Augusto F. de Oliveira | Zendy; Mikolai Fajer | Zendy; William Sinko | Zendy; J. Andrew McCammon | Zendy

Open Access

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

Author(s) -

Mehrnoosh Arrar,

César Augusto F. de Oliveira,

Mikolai Fajer,

William Sinko,

J. Andrew McCammon

Publication year - 2012

Publication title -

journal of chemical theory and computation

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.001

H-Index - 185

eISSN - 1549-9626

pISSN - 1549-9618

DOI - 10.1021/ct300896h

Subject(s) - replica , maxima and minima , hamiltonian (control theory) , statistical physics , molecular dynamics , umbrella sampling , sampling (signal processing) , limit (mathematics) , energy (signal processing) , physics , computer science , quantum mechanics , mathematical optimization , mathematics , art , mathematical analysis , detector , optics , visual arts

Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange framework (w-REXAMD). We show that for a case in which multiple conformations are separated by large free energy barriers, w-REXAMD is a useful enhanced sampling technique, without any necessary reweighting.

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