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Accurate multiple time step in biased molecular simulations

Ferrarotti, M. J.
•
Bottaro, Sandro
•
Perez Villa, Andrea
•
Bussi, Giovanni
2015
  • journal article

Periodico
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Abstract
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed. The implementation is simple and allows a speed up when expensive collective variables are employed. The gain can be substantial when using massively parallel or GPU-based molecular dynamics software. Moreover, a theoretical framework to assess the sampling accuracy is introduced, which can be used to assess the choice of the integration time step in both single and multiple time step biased simulations.
DOI
10.1021/ct5007086
WOS
WOS:000348085400017
Archivio
http://hdl.handle.net/20.500.11767/11876
info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84921409453
https://arxiv.org/abs/1412.3916
Diritti
closed access
Soggetti
  • free-energy

  • force-field

  • dynamics simulation

  • pulling simulation

  • nucleic-acid

  • temperature

  • distribution

  • algorithm

  • mechanic

  • efficient

  • Settore FIS/03 - Fisi...

Scopus© citazioni
19
Data di acquisizione
Jun 7, 2022
Vedi dettagli
Web of Science© citazioni
25
Data di acquisizione
Mar 19, 2024
Visualizzazioni
3
Data di acquisizione
Apr 19, 2024
Vedi dettagli
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