Literature DB >> 21828594

Polarization effects in molecular mechanical force fields.

Piotr Cieplak1, François-Yves Dupradeau, Yong Duan, Junmei Wang.   

Abstract

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations.

Entities:  

Year:  2009        PMID: 21828594      PMCID: PMC4020598          DOI: 10.1088/0953-8984/21/33/333102

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  84 in total

1.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

3.  Effective Born radii in the generalized Born approximation: the importance of being perfect.

Authors:  Alexey Onufriev; David A Case; Donald Bashford
Journal:  J Comput Chem       Date:  2002-11-15       Impact factor: 3.376

4.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

5.  Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

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

6.  Solvent reorganization energies in A-DNA, B-DNA, and rhodamine 6G-DNA complexes from molecular dynamics simulations with a polarizable force field.

Authors:  Egor Vladimirov; Anela Ivanova; Notker Rösch
Journal:  J Phys Chem B       Date:  2009-04-02       Impact factor: 2.991

7.  Calculations of the thermal conductivities of ionic materials by simulation with polarizable interaction potentials.

Authors:  Norikazu Ohtori; Mathieu Salanne; Paul A Madden
Journal:  J Chem Phys       Date:  2009-03-14       Impact factor: 3.488

8.  The implementation of a fast and accurate QM/MM potential method in Amber.

Authors:  Ross C Walker; Michael F Crowley; David A Case
Journal:  J Comput Chem       Date:  2008-05       Impact factor: 3.376

9.  Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration.

Authors:  Carolyn A Fitch; Daniel A Karp; Kelly K Lee; Wesley E Stites; Eaton E Lattman; Bertrand García-Moreno E
Journal:  Biophys J       Date:  2002-06       Impact factor: 4.033

10.  Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

Authors:  Pedro E M Lopes; Guillaume Lamoureux; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2009-09       Impact factor: 3.376

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  66 in total

1.  Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

Authors:  Junmei Wang; Tingjun Hou
Journal:  J Comput Chem       Date:  2011-09-22       Impact factor: 3.376

2.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

3.  AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-06-11       Impact factor: 6.006

4.  Computational and Experimental Studies of Inhibitor Design for Aldolase A.

Authors:  Rui Qi; Brandon Walker; Zhifeng Jing; Maiya Yu; Gabriel Stancu; Ramakrishna Edupuganti; Kevin N Dalby; Pengyu Ren
Journal:  J Phys Chem B       Date:  2019-07-03       Impact factor: 2.991

Review 5.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

6.  Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

Authors:  Jiří Šponer; Judit E Šponer; Anton I Petrov; Neocles B Leontis
Journal:  J Phys Chem B       Date:  2010-11-04       Impact factor: 2.991

Review 7.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

Review 8.  Molecular modeling of nucleic acid structure: energy and sampling.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-05

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

Authors:  Jing Huang; Justin A Lemkul; Peter K Eastman; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-05-04       Impact factor: 3.376

10.  Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations.

Authors:  Caitlin E Scott; Peter M Kekenes-Huskey
Journal:  Biophys J       Date:  2016-03-08       Impact factor: 4.033

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