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. © 2013 by the author; licensee MDPI, Basel, Switzerland.

Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration / Abrams, C.; Bussi, G.. - In: ENTROPY. - ISSN 1099-4300. - 16:1(2014), pp. 163-199. [10.3390/e16010163]

Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration

Bussi, G.
2014-01-01

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. © 2013 by the author; licensee MDPI, Basel, Switzerland.
2014
16
1
163
199
10.3390/e16010163
https://arxiv.org/abs/1401.0387
Abrams, C.; Bussi, G.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/15914
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