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Entropy 2014, 16(1), 163-199; doi:10.3390/e16010163
Article

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

1,*  and 2
1 Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA 2 Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
* Author to whom correspondence should be addressed.
Received: 13 September 2013 / Revised: 7 November 2013 / Accepted: 11 November 2013 / Published: 27 December 2013
(This article belongs to the Special Issue Molecular Dynamics Simulation)
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Abstract

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.
Keywords: collective variables; free energy; blue-moon sampling; adaptive-biasing force algorithm; temperature-acceleration; umbrella sampling; metadynamics collective variables; free energy; blue-moon sampling; adaptive-biasing force algorithm; temperature-acceleration; umbrella sampling; metadynamics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Abrams, C.; Bussi, G. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. Entropy 2014, 16, 163-199.

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