Literature DB >> 33868909

Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM.

Matthew Harger1, Pengyu Ren1.   

Abstract

The Tinker-OpenMM package for AMOEBA molecular dynamics on GPU has long been limited to the Monte Carlo barostat due to the lack of virial calculation. In this paper, we report the calculation of the internal virial for the AMOEBA forcefield. This constitutes the first GPU implementation of a polarizable internal virial. This is followed by the implementation of the Berendsen barostat into Tinker-OpenMM as a demonstration of the capability of Tinker-OpenMM to calculate the virial with sufficient accuracy to enable pressure control. These additions enable the further improvement of Tinker-OpenMM to include a wide range of virial-based barostat algorithms.

Entities:  

Year:  2019        PMID: 33868909      PMCID: PMC8049534          DOI: 10.1016/j.rechem.2019.100004

Source DB:  PubMed          Journal:  Results Chem        ISSN: 2211-7156


  13 in total

1.  Piezotolerance as a metabolic engineering tool for the biosynthesis of natural products.

Authors:  Phillip C Wright; Robin E Westacott; Adam M Burja
Journal:  Biomol Eng       Date:  2003-07

2.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

3.  Canonical dynamics: Equilibrium phase-space distributions.

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

4.  OpenMM: A Hardware Independent Framework for Molecular Simulations.

Authors:  Peter Eastman; Vijay S Pande
Journal:  Comput Sci Eng       Date:  2015-07-01       Impact factor: 2.080

5.  Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Authors:  Johnny C Wu; Jean-Philip Piquemal; Robin Chaudret; Peter Reinhardt; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2010-07-13       Impact factor: 6.006

6.  Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

Authors:  Matthew Harger; Daniel Li; Zhi Wang; Kevin Dalby; Louis Lagardère; Jean-Philip Piquemal; Jay Ponder; Pengyu Ren
Journal:  J Comput Chem       Date:  2017-06-10       Impact factor: 3.376

Review 7.  Enzymes from piezophiles.

Authors:  Toshiko Ichiye
Journal:  Semin Cell Dev Biol       Date:  2018-02-01       Impact factor: 7.727

8.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

9.  Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology.

Authors:  José A Caro; A Joshua Wand
Journal:  Methods       Date:  2018-06-30       Impact factor: 3.608

10.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Authors:  Peter Eastman; Jason Swails; John D Chodera; Robert T McGibbon; Yutong Zhao; Kyle A Beauchamp; Lee-Ping Wang; Andrew C Simmonett; Matthew P Harrigan; Chaya D Stern; Rafal P Wiewiora; Bernard R Brooks; Vijay S Pande
Journal:  PLoS Comput Biol       Date:  2017-07-26       Impact factor: 4.475

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