Literature DB >> 26580355

GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

Robert E Duke1, Oleg N Starovoytov1, Jean-Philip Piquemal2,3, G Andrés Cisneros1.   

Abstract

GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed.

Entities:  

Year:  2014        PMID: 26580355      PMCID: PMC5207213          DOI: 10.1021/ct500050p

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  36 in total

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2.  The GROMOS software for biomolecular simulation: GROMOS05.

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Authors:  Volodymyr Babin; Jason Baucom; Thomas A Darden; Celeste Sagui
Journal:  J Phys Chem B       Date:  2006-06-15       Impact factor: 2.991

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Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

6.  Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

Authors:  G A Cisneros; S Na-Im Tholander; O Parisel; T A Darden; D Elking; L Perera; J-P Piquemal
Journal:  Int J Quantum Chem       Date:  2008       Impact factor: 2.444

7.  Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.

Authors:  Zhenyu Lu; Nengjie Zhou; Qin Wu; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2011-12-13       Impact factor: 6.006

8.  Aqueous imidazole solutions: a structural perspective from simulations with high-rank electrostatic multipole moments.

Authors:  Steven Y Liem; Majeed S Shaik; Paul L A Popelier
Journal:  J Phys Chem B       Date:  2011-09-09       Impact factor: 2.991

9.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Authors:  Wangshen Xie; Modesto Orozco; Donald G Truhlar; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2009-02-17       Impact factor: 6.006

10.  From dimer to condensed phases at extreme conditions: accurate predictions of the properties of water by a Gaussian charge polarizable model.

Authors:  Patrice Paricaud; Milan Predota; Ariel A Chialvo; Peter T Cummings
Journal:  J Chem Phys       Date:  2005-06-22       Impact factor: 3.488

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  28 in total

1.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

2.  LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Authors:  Eric G Kratz; Alice R Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Comput Chem       Date:  2016-01-18       Impact factor: 3.376

3.  Classical Pauli repulsion: An anisotropic, atomic multipole model.

Authors:  Joshua A Rackers; Jay W Ponder
Journal:  J Chem Phys       Date:  2019-02-28       Impact factor: 3.488

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis.

Authors:  Nengjie Zhou; Zhenyu Lu; Qin Wu; Yingkai Zhang
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

6.  Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.

Authors:  Haixin Wei; Ruxi Qi; Junmei Wang; Piotr Cieplak; Yong Duan; Ray Luo
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

7.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

8.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

9.  An optimized charge penetration model for use with the AMOEBA force field.

Authors:  Joshua A Rackers; Qiantao Wang; Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  Phys Chem Chem Phys       Date:  2016-12-21       Impact factor: 3.676

10.  QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

Authors:  Hatice Gökcan; Eric Kratz; Thomas A Darden; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Phys Chem Lett       Date:  2018-05-23       Impact factor: 6.475

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