title: w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations.
abstract: 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.
authors: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, United States.
authors: Mehrnoosh
authors: M
authors: Arrar
authors: Cesar Augusto F
authors: CA
authors: de Oliveira
authors: Mikolai
authors: M
authors: Fajer
authors: William
authors: W
authors: Sinko
authors: J Andrew
authors: JA
authors: McCammon