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Constant pressure hybrid Monte Carlo simulations in GROMACS

descriptionPublicationkeyboard_double_arrow_right Article 19 Nov 2014 Spain Publisher:Springer Science and Business Media LLCJournal:Journal of Molecular Modeling, volume 20 (issn: 1610-2940, eissn: 0948-5023,

Authors: Elena Akhmatskaya; Elena Akhmatskaya; Bruno Escribano; Mario Fernández-Pendás; Tijana Radivojevic;

doi: 10.1007/s00894-014-2487-y

pmid: 25408507

handle: 20.500.11824/167

Constant pressure hybrid Monte Carlo simulations in GROMACS

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Abstract

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Generalized Hybrid Monte Carlo methods are designed to maintain constant temperature and volume and extending their functionality to preserving pressure is not trivial. The theoretical formulation of NPT-GSHMC was previously introduced. Our main contribution is the implementation of this methodology in the GROMACS molecular simulation package and the evaluation of properties of NPT-GSHMC, such as accuracy, performance, effectiveness for real physical systems in comparison with well-established molecular simulation techniques. Benchmarking tests are presented and the obtained preliminary results are promising. For the first time, the generalized hybrid Monte Carlo simulations at constant pressure are available within the popular open source molecular dynamics software package.

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Spain

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Keywords

barostat, accuracy, constant pressure, temperature, methodology, oscillation, simulation, theoretical study, villin, Article, molecular dynamics, Monte Carlo method, pressure, priority journal, Generalized Shadow Hybrid Monte Carlo, controlled study, measurement accuracy, quality control, generalized shadow hybrid monte carl simulation

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