Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

The Journal of Physical Chemistry A ◽

10.1021/acs.jpca.0c05461 ◽

2020 ◽

Vol 124 (37) ◽

pp. 7585-7597

Author(s):

Ivan Scivetti ◽

Kakali Sen ◽

Alin M. Elena ◽

Ilian Todorov

Keyword(s):

Molecular Dynamics ◽

Constant Pressure ◽

Force Fields ◽

Valence Bond ◽

Reactive Molecular Dynamics ◽

Empirical Valence Bond ◽

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A High-Throughput Multiobjective Genetic-Algorithm Workflow for In Situ Training of Reactive Molecular-Dynamics Force Fields

24th High Performance Computing Symposium ◽

10.22360/springsim.2016.hpc.004 ◽

2016 ◽

Keyword(s):

Genetic Algorithm ◽

Molecular Dynamics ◽

High Throughput ◽

Force Fields ◽

Multiobjective Genetic Algorithm ◽

Reactive Molecular Dynamics ◽

In Situ Training

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Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems

Journal of Molecular Graphics and Modelling ◽

10.1016/s1093-3263(98)80006-5 ◽

1998 ◽

Vol 16 (4-6) ◽

pp. 213-225 ◽

Author(s):

John Marelius ◽

Karin Kolmodin ◽

Isabella Feierberg ◽

Johan Åqvist

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Valence Bond ◽

Free Energy Calculations ◽

Biomolecular Systems ◽

Energy Calculations ◽

Empirical Valence Bond

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Empirical Valence-Bond Models Based on Polarizable Force Fields for Infrared Spectroscopy

Theory and Applications of the Empirical Valence Bond Approach ◽

10.1002/9781119245544.ch5 ◽

2017 ◽

pp. 121-144

Author(s):

Florian Thaunay ◽

Florent Calvo ◽

Gilles Ohanessian ◽

Carine Clavaguéra

Keyword(s):

Infrared Spectroscopy ◽

Force Fields ◽

Valence Bond ◽

Polarizable Force Fields ◽

Empirical Valence Bond

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Density functional based parametrization of a valence bond method and its applications in quantum-classical molecular dynamics simulations of enzymatic reactions

International Journal of Quantum Chemistry ◽

10.1002/(sici)1097-461x(1996)60:6<1143::aid-qua4>3.0.co;2-# ◽

1996 ◽

Vol 60 (6) ◽

pp. 1143-1164 ◽

Author(s):

P. Grochowski ◽

B. Lesyng ◽

P. Ba?a ◽

J. A. McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Valence Bond ◽

Enzymatic Reactions ◽

Classical Molecular Dynamics ◽

Dynamics Simulations ◽

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A linear-scaling self-consistent generalization of the multistate empirical valence bond method for multiple excess protons in aqueous systems

The Journal of Chemical Physics ◽

10.1063/1.1881092 ◽

2005 ◽

Vol 122 (14) ◽

pp. 144105 ◽

Author(s):

Feng Wang ◽

Gregory A. Voth

Keyword(s):

Valence Bond ◽

Linear Scaling ◽

Aqueous Systems ◽

Empirical Valence Bond ◽

Self Consistent ◽

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VBDFT(s): a Hückel-type semi-empirical valence bond method scaled to density functional energies. Application to linear polyenes

Chemical Physics Letters ◽

10.1016/s0009-2614(98)00684-8 ◽

1998 ◽

Vol 292 (1-2) ◽

pp. 7-14 ◽

Author(s):

Wei Wu ◽

Shi-jun Zhong ◽

Sason Shaik

Keyword(s):

Density Functional ◽

Valence Bond ◽

Empirical Valence Bond ◽

Linear Polyenes ◽

Semi Empirical ◽

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Reactive molecular dynamics for the [Cl–CH 3 –Br] − reaction in the gas phase and in solution: a comparative study using empirical and neural network force fields

Electronic Structure ◽

10.1088/2516-1075/ab1edb ◽

2019 ◽

Vol 1 (2) ◽

pp. 024002 ◽

Author(s):

Sebastian Brickel ◽

Akshaya K Das ◽

Oliver T Unke ◽

Haydar T Turan ◽

Markus Meuwly

Keyword(s):

Neural Network ◽

Molecular Dynamics ◽

Comparative Study ◽

Gas Phase ◽

Force Fields ◽

Reactive Molecular Dynamics

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A Molecular Dynamics−Empirical Valence Bond Study of an SN2 Reaction at the Water/Chloroform Interface

The Journal of Physical Chemistry C ◽

10.1021/jp9093645 ◽

2009 ◽

Vol 114 (2) ◽

pp. 1154-1163 ◽

Author(s):

Katherine V. Nelson ◽

Ilan Benjamin

Keyword(s):

Molecular Dynamics ◽

Valence Bond ◽

Empirical Valence Bond ◽

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Biasing the Center of Charge in Molecular Dynamics Simulations with Empirical Valence Bond Models: Free Energetics of an Excess Proton in a Water Droplet

The Journal of Physical Chemistry B ◽

10.1021/jp8048422 ◽

2008 ◽

Vol 112 (28) ◽

pp. 8425-8425

Author(s):

Jürgen Köfinger ◽

Christoph Dellago

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Water Droplet ◽

Valence Bond ◽

Empirical Valence Bond ◽

Dynamics Simulations

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Investigating Hydroxide Anion Interfacial Activity by Classical and Multistate Empirical Valence Bond Molecular Dynamics Simulations

The Journal of Physical Chemistry A ◽

10.1021/jp900290y ◽

2009 ◽

Vol 113 (22) ◽

pp. 6356-6364 ◽

Author(s):

Collin D. Wick ◽

Liem X. Dang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Valence Bond ◽

Interfacial Activity ◽

Hydroxide Anion ◽

Empirical Valence Bond ◽

Dynamics Simulations

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