Literature DB >> 29119281

"Swarm relaxation": Equilibrating a large ensemble of computer simulations.

Shahrazad M A Malek1, Richard K Bowles2, Ivan Saika-Voivod1, Francesco Sciortino3, Peter H Poole4.   

Abstract

It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of M independent simulations (a "swarm"), each of which is relaxed to equilibrium. We show that if M is of order [Formula: see text], we can monitor the swarm's relaxation to equilibrium, and confirm its attainment, within [Formula: see text], where [Formula: see text] is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of M final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.

Keywords:  Topical issue: Advances in Computational Methods for Soft Matter Systems

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Substances:

Year:  2017        PMID: 29119281     DOI: 10.1140/epje/i2017-11588-2

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  14 in total

1.  Crossover (or Kovacs) effect in an aging molecular liquid.

Authors:  Stefano Mossa; Francesco Sciortino
Journal:  Phys Rev Lett       Date:  2004-01-30       Impact factor: 9.161

2.  A general purpose model for the condensed phases of water: TIP4P/2005.

Authors:  J L F Abascal; C Vega
Journal:  J Chem Phys       Date:  2005-12-15       Impact factor: 3.488

3.  Relation between local diffusivity and local inherent structures in the Kob-Andersen Lennard-Jones model.

Authors:  Emilia La Nave; Srikanth Sastry; Francesco Sciortino
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-11-14

4.  Canonical dynamics: Equilibrium phase-space distributions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

5.  Dynamical behavior near a liquid-liquid phase transition in simulations of supercooled water.

Authors:  Peter H Poole; Stephen R Becker; Francesco Sciortino; Francis W Starr
Journal:  J Phys Chem B       Date:  2011-08-26       Impact factor: 2.991

6.  Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

Authors:  L S Caves; J D Evanseck; M Karplus
Journal:  Protein Sci       Date:  1998-03       Impact factor: 6.725

7.  Metastable liquid-liquid transition in a molecular model of water.

Authors:  Jeremy C Palmer; Fausto Martelli; Yang Liu; Roberto Car; Athanassios Z Panagiotopoulos; Pablo G Debenedetti
Journal:  Nature       Date:  2014-06-19       Impact factor: 49.962

8.  Two-state thermodynamics of the ST2 model for supercooled water.

Authors:  Vincent Holten; Jeremy C Palmer; Peter H Poole; Pablo G Debenedetti; Mikhail A Anisimov
Journal:  J Chem Phys       Date:  2014-03-14       Impact factor: 3.488

9.  How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

Authors:  A Elofsson; L Nilsson
Journal:  J Mol Biol       Date:  1993-10-20       Impact factor: 5.469

10.  On the calculation of equilibrium thermodynamic properties from molecular dynamics.

Authors:  Peter V Coveney; Shunzhou Wan
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

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  3 in total

1.  Topical Issue on Advances in Computational Methods for Soft Matter Systems.

Authors:  Lorenzo Rovigatti; Flavio Romano; John Russo
Journal:  Eur Phys J E Soft Matter       Date:  2018-08-29       Impact factor: 1.890

2.  Topical Issue on Dielectric Spectroscopy Applied to Soft Matter.

Authors:  Simone Napolitano
Journal:  Eur Phys J E Soft Matter       Date:  2020-01-23       Impact factor: 1.890

3.  Thermodynamic and structural anomalies of water nanodroplets.

Authors:  Shahrazad M A Malek; Peter H Poole; Ivan Saika-Voivod
Journal:  Nat Commun       Date:  2018-06-19       Impact factor: 14.919

  3 in total

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