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

Entropy

Cameron Abrams¹ 

[1] Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA

关键词: collective variables;    free energy;    blue-moon sampling;    adaptive-biasing force algorithm;    temperature-acceleration;    umbrella sampling;    metadynamics;   

DOI  :  10.3390/e16010163

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland