A Generalized Linear Response Framework for Expanded Ensemble and Replica Exchange Simulations

Overview

Journal J Chem Phys

Publisher American Institute of Physics

Specialties Biophysics
Chemistry

Date 2018 Aug 24

PMID 30134700

Citations 2

Authors

Brian K Radak

Donghyuk Suh

Benoit Roux

Affiliations

Soon will be listed here.

Abstract

Expanded ensemble simulation is a powerful technique for enhancing sampling over a range of thermodynamic parameters. However, although the premise is relatively simple, running successful simulations in practice still presents something of an challenge. Three main difficulties exist: (1) the selection of the thermodynamic states, (2) the selection of the sampling weights, and (3) efficient sampling of the expanded parameter space. Here we consider these problems in the context of a pairwise linear response approach to the work fluctuation theorem. The approach offers comprehensive tactics for addressing the three difficulties and can be used as either an alternative or a complement to replica exchange simulations. Importantly, the results are trivially implemented for multi-dimensional parameter spaces and they recover results from the literature aimed at the special cases of simulated/parallel tempering and replica exchange umbrella sampling. Illustrative examples are shown using the NAMD simulation engine.

Citing Articles

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Lee T, Allen B, Giese T, Guo Z, Li P, Lin C J Chem Inf Model. 2020; 60(11):5595-5623.

PMID: 32936637 PMC: 7686026. DOI: 10.1021/acs.jcim.0c00613.

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems.

Lazim R, Suh D, Choi S Int J Mol Sci. 2020; 21(17).

PMID: 32882859 PMC: 7504087. DOI: 10.3390/ijms21176339.

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