Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

Steffen Lindert; Denis Bucher; Peter Eastman; Vijay Pande; J. Andrew McCammon

doi:10.1021/ct400514p

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

Journal of Chemical Theory and Computation ◽

10.1021/ct400514p ◽

2013 ◽

Vol 9 (11) ◽

pp. 4684-4691 ◽

Cited By ~ 28

Author(s):

Steffen Lindert ◽

Denis Bucher ◽

Peter Eastman ◽

Vijay Pande ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Graphics Processing Units ◽

Polarizable Force Field ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations ◽

Graphics Processing

Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

10.1063/1.4938814 ◽

2015 ◽

Author(s):

Nazanin Davari ◽

Shokouh Haghdani ◽

Per-Olof Åstrand

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Local Field ◽

Frequency Dependent ◽

Polarizable Force Field ◽

Dielectric Liquids ◽

Dynamics Simulations

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

Journal of Computational Chemistry ◽

10.1002/jcc.25339 ◽

2018 ◽

Vol 39 (21) ◽

pp. 1682-1689 ◽

Cited By ~ 34

Author(s):

Jing Huang ◽

Justin A. Lemkul ◽

Peter K. Eastman ◽

Alexander D. MacKerell

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Polarizable Force Field ◽

Dynamics Simulations

Polarizable Force Field Development and Molecular Dynamics Simulations of Ionic Liquids

The Journal of Physical Chemistry B ◽

10.1021/jp905220k ◽

2009 ◽

Vol 113 (33) ◽

pp. 11463-11478 ◽

Cited By ~ 420

Author(s):

Oleg Borodin

Keyword(s):

Molecular Dynamics ◽

Ionic Liquids ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Polarizable Force Field ◽

Field Development ◽

Force Field Development ◽

Dynamics Simulations

The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures

Molecular Physics ◽

10.1080/00268970701444631 ◽

2007 ◽

Vol 105 (13-14) ◽

pp. 1861-1881 ◽

Cited By ~ 44

Author(s):

D. P. Geerke ◽

W. F. van Gunsteren

Keyword(s):

Molecular Dynamics ◽

Ethylene Glycol ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Field Parameter ◽

Pure Liquid ◽

Aqueous Mixtures ◽

Polarizable Force Field ◽

Force Field Parameter ◽

Dynamics Simulations

Solvent Reorganization Energies in A-DNA, B-DNA, and Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations with a Polarizable Force Field

The Journal of Physical Chemistry B ◽

10.1021/jp809774q ◽

2009 ◽

Vol 113 (13) ◽

pp. 4425-4434 ◽

Cited By ~ 17

Author(s):

Egor Vladimirov ◽

Anela Ivanova ◽

Notker Rösch

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Rhodamine 6G ◽

Dna Complexes ◽

Polarizable Force Field ◽

Reorganization Energies ◽

Dynamics Simulations

Shear Viscosity of Liquid-Phase Yukawa Plasmas from Molecular Dynamics Simulations on Graphics Processing Units

Contributions to Plasma Physics ◽

10.1002/ctpp.201100083 ◽

2012 ◽

Vol 52 (3) ◽

pp. 194-198 ◽

Cited By ~ 5

Author(s):

Á. Budea ◽

A. Derzsi ◽

P. Hartmann ◽

Z. Donkó

Keyword(s):

Molecular Dynamics ◽

Liquid Phase ◽

Molecular Dynamics Simulations ◽

Shear Viscosity ◽

Graphics Processing Units ◽

Dynamics Simulations ◽

Graphics Processing

Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00666 ◽

2019 ◽

Vol 59 (11) ◽

pp. 4855-4867 ◽

Cited By ~ 4

Author(s):

Gábor Balogh ◽

Tamás Gyöngyösi ◽

István Timári ◽

Mihály Herczeg ◽

Anikó Borbás ◽

...

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

Accelerated Molecular Dynamics ◽

Force Field Parameters ◽

Dynamics Simulations

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.7b00068 ◽

2017 ◽

Vol 13 (5) ◽

pp. 2072-2085 ◽

Cited By ~ 33

Author(s):

Justin A. Lemkul ◽

Alexander D. MacKerell

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Duplex Dna ◽

Polarizable Force Field ◽

Dynamics Simulations

Development of a Polarizable Force Field for Molecular Dynamics Simulations of Lithium-Ion Battery Electrolytes: Sulfone-Based Solvents and Lithium Salts

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.1c05744 ◽

2021 ◽

Author(s):

Oleg N. Starovoytov

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Lithium Ion Battery ◽

Lithium Ion ◽

Lithium Salts ◽

Polarizable Force Field ◽

Dynamics Simulations

Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

Physical Chemistry Chemical Physics ◽

10.1039/c5cp02270c ◽

2015 ◽

Vol 17 (39) ◽

pp. 25968-25977 ◽

Cited By ~ 11

Author(s):

Florian Thaunay ◽

Jean-Pierre Dognon ◽

Gilles Ohanessian ◽

Carine Clavaguéra

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Infrared Spectra ◽

Finite Temperature ◽

Vibrational Mode ◽

Vibrational Modes ◽

Polarizable Force Field ◽

Dynamics Simulations ◽

Mode Assignment

The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.