Literature DB >> 16774315

Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations.

E A Koopman1, C P Lowe.   

Abstract

The Lowe-Andersen thermostat is a momentum conserving and Galilean invariant analog of the Andersen thermostat. Like the Andersen thermostat it has the advantage of being local. We show that by using a minimal thermostat interaction radius in a molecular dynamics simulation, it perturbs the system dynamics to a far lesser extent than the Andersen method. This alleviates a well known drawback of the Andersen thermostat by allowing high thermostatting rates without the penalty of significantly suppressed diffusion in the system.

Year:  2006        PMID: 16774315     DOI: 10.1063/1.2198824

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


  32 in total

1.  Modeling thermophoretic effects in solid-state nanopores.

Authors:  Maxim Belkin; Shu-Han Chao; Gino Giannetti; Aleksei Aksimentiev
Journal:  J Comput Electron       Date:  2014-12-01       Impact factor: 1.807

2.  Quantum mechanical force field for water with explicit electronic polarization.

Authors:  Jaebeom Han; Michael J M Mazack; Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

3.  A simple molecular mechanics integrator in mixed rigid body and dihedral angle space.

Authors:  Andreas Vitalis; Rohit V Pappu
Journal:  J Chem Phys       Date:  2014-07-21       Impact factor: 3.488

4.  High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.

Authors:  Wei Jiang; David J Hardy; James C Phillips; Alexander D Mackerell; Klaus Schulten; Benoît Roux
Journal:  J Phys Chem Lett       Date:  2011       Impact factor: 6.475

5.  Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence.

Authors:  Swati Bhattacharya; Ian M Derrington; Mikhail Pavlenok; Michael Niederweis; Jens H Gundlach; Aleksei Aksimentiev
Journal:  ACS Nano       Date:  2012-07-13       Impact factor: 15.881

6.  Graphene Nanopores for Protein Sequencing.

Authors:  James Wilson; Leila Sloman; Zhiren He; Aleksei Aksimentiev
Journal:  Adv Funct Mater       Date:  2016-06-09       Impact factor: 18.808

7.  Modulation of Molecular Flux Using a Graphene Nanopore Capacitor.

Authors:  Manish Shankla; Aleksei Aksimentiev
Journal:  J Phys Chem B       Date:  2017-01-17       Impact factor: 2.991

8.  Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics.

Authors:  David S Cerutti; Robert Duke; Peter L Freddolino; Hao Fan; Terry P Lybrand
Journal:  J Chem Theory Comput       Date:  2008-10-14       Impact factor: 6.006

9.  Investigation of mechanisms of viscoelastic behavior of collagen molecule.

Authors:  Hossein Ghodsi; Kurosh Darvish
Journal:  J Mech Behav Biomed Mater       Date:  2015-07-26

10.  Characterization of the viscoelastic behavior of a simplified collagen micro-fibril based on molecular dynamics simulations.

Authors:  Hossein Ghodsi; Kurosh Darvish
Journal:  J Mech Behav Biomed Mater       Date:  2016-06-11
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