Literature DB >> 19239278

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling.

Giovanni Bussi1, Tatyana Zykova-Timan, Michele Parrinello.   

Abstract

The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The technical aspects concerning the derivation of the integration scheme and the conservation laws are discussed in detail. The efficiency of the barostat is examined in Lennard-Jones solid and liquid near the triple point and compared to the deterministic Nose-Hoover and the stochastic Langevin methods. In particular, the dependence of the sampling efficiency on the choice of the thermostat and barostat relaxation times is systematically analyzed.

Year:  2009        PMID: 19239278     DOI: 10.1063/1.3073889

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  65 in total

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Authors:  Erik J Alred; Emily G Scheele; Workalemahu M Berhanu; Ulrich H E Hansmann
Journal:  J Chem Phys       Date:  2014-11-07       Impact factor: 3.488

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Journal:  Biophys J       Date:  2012-11-20       Impact factor: 4.033

8.  Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes.

Authors:  Mary Pitman; Yamini Dalal; Garegin A Papoian
Journal:  Biophys J       Date:  2020-02-12       Impact factor: 4.033

9.  Mutations and seeding of amylin fibril-like oligomers.

Authors:  Nathan A Bernhardt; Workalemahu M Berhanu; Ulrich H E Hansmann
Journal:  J Phys Chem B       Date:  2013-12-02       Impact factor: 2.991

10.  Ligand binding to anti-cancer target CD44 investigated by molecular simulations.

Authors:  Tin Trung Nguyen; Duy Phuoc Tran; Zung Hoang; Paolo Carloni; Phuc Van Pham; Chuong Nguyen; Mai Suan Li
Journal:  J Mol Model       Date:  2016-06-24       Impact factor: 1.810

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