Literature DB >> 12548718

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations.

George A Kaminski1, Richard A Friesner, Ruhong Zhou.   

Abstract

We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH(3)SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 267-276, 2003

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Year:  2003        PMID: 12548718     DOI: 10.1002/jcc.10170

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  18 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.  Interfacial structure, thermodynamics, and electrostatics of aqueous methanol solutions via molecular dynamics simulations using charge equilibration models.

Authors:  Sandeep Patel; Yang Zhong; Brad A Bauer; Joseph E Davis
Journal:  J Phys Chem B       Date:  2009-07-09       Impact factor: 2.991

3.  Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model.

Authors:  Ity Sharma; George A Kaminski
Journal:  J Comput Chem       Date:  2012-07-19       Impact factor: 3.376

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 modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications.

Authors:  Pedro E M Lopes; Benoit Roux; Alexander D Mackerell
Journal:  Theor Chem Acc       Date:  2009-09       Impact factor: 1.702

6.  Developing multisite empirical force field models for Pt(II) and cisplatin.

Authors:  John P Cvitkovic; George A Kaminski
Journal:  J Comput Chem       Date:  2016-11-11       Impact factor: 3.376

7.  Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone.

Authors:  Sergei Y Ponomarev; George A Kaminski
Journal:  J Chem Theory Comput       Date:  2011-05-10       Impact factor: 6.006

8.  Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations.

Authors:  George A Kaminski; Sergei Y Ponomarev; Aibing B Liu
Journal:  J Chem Theory Comput       Date:  2009-10-05       Impact factor: 6.006

9.  Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

Authors:  Xinbi Li; Sergei Y Ponomarev; Qina Sa; Daniel L Sigalovsky; George A Kaminski
Journal:  J Comput Chem       Date:  2013-02-19       Impact factor: 3.376

10.  Effects of lysine substitution on stability of polyalanine alpha-helix.

Authors:  Sergei Y Ponomarev; Qina Sa; George A Kaminski
Journal:  J Chem Theory Comput       Date:  2012-10-02       Impact factor: 6.006

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