Literature DB >> 14696069

Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.

Jirí Kolafa1.   

Abstract

An improved method for classic molecular dynamics of polarizable molecules is proposed. The method uses a predictor, one evaluation of the electrostatic field per integration step, and relaxation (damping). The self-consistent solution is approximated with error of the second order (with respect to the timestep). The time reversibility (long-time energy conservation) error is of the (2n - 1)th order, where n is the predictor length. The method is easy to implement, efficient, accurate, and suitable for any model of polarizability. Copyright 2003 Wiley Periodicals, Inc.

Year:  2004        PMID: 14696069     DOI: 10.1002/jcc.10385

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


  12 in total

1.  Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

Authors:  Guishan Zheng; Anders M N Niklasson; Martin Karplus
Journal:  J Chem Phys       Date:  2011-07-28       Impact factor: 3.488

2.  Polarizable molecular dynamics in a polarizable continuum solvent.

Authors:  Filippo Lipparini; Louis Lagardère; Christophe Raynaud; Benjamin Stamm; Eric Cancès; Benedetta Mennucci; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

3.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

Authors:  Louis Lagardère; Filippo Lipparini; Étienne Polack; Benjamin Stamm; Éric Cancès; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2014-02-28       Impact factor: 6.006

4.  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

5.  A comparison of sodium and hydrogen halides at the air-water interface.

Authors:  Collin D Wick
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

6.  Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions.

Authors:  Zhenyu Lu; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

7.  Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations.

Authors:  Léa El Khoury; Frédéric Célerse; Louis Lagardère; Luc-Henri Jolly; Etienne Derat; Zeina Hobaika; Richard G Maroun; Pengyu Ren; Serge Bouaziz; Nohad Gresh; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2020-03-30       Impact factor: 6.006

8.  A coupled polarization-matrix inversion and iteration approach for accelerating the dipole convergence in a polarizable potential function.

Authors:  Wangshen Xie; Jingzhi Pu; Jiali Gao
Journal:  J Phys Chem A       Date:  2009-03-12       Impact factor: 2.781

9.  Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations.

Authors:  Félix Aviat; Antoine Levitt; Benjamin Stamm; Yvon Maday; Pengyu Ren; Jay W Ponder; Louis Lagardère; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2016-12-08       Impact factor: 6.006

10.  Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Authors:  Louis Lagardère; Luc-Henri Jolly; Filippo Lipparini; Félix Aviat; Benjamin Stamm; Zhifeng F Jing; Matthew Harger; Hedieh Torabifard; G Andrés Cisneros; Michael J Schnieders; Nohad Gresh; Yvon Maday; Pengyu Y Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2017-11-27       Impact factor: 9.825

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