Literature DB >> 31865706

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential.

Chengwen Liu1, Jean-Philip Piquemal1,2,3, Pengyu Ren1.   

Abstract

Molecular dynamics (MD) simulations employing classical force fields (FFs) have been widely used to model molecular systems. The important ingredient of the current FFs, atomic charge, remains fixed during MD simulations despite the atomic environment or local geometry changes. This approximation hinders the transferability of the potential being used in multiple phases. Here we implement a geometry-dependent charge flux (GDCF) model into the multipole-based AMOEBA+ polarizable potential. The CF in the current work explicitly depends on the local geometry (bond and angle) of the molecule. To our knowledge, this is the first study that derives energy and force expressions due to GDCF in a multipole-based polarizable FF framework. Due to the inclusion of GDCF, the AMOEBA+ water model is noticeably improved in terms of describing the monomer properties, cluster binding/interaction energy, and a variety of liquid properties, including the infrared spectra that previous flexible water models were not able to capture.

Entities:  

Year:  2019        PMID: 31865706      PMCID: PMC7384396          DOI: 10.1021/acs.jpclett.9b03489

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  32 in total

1.  Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

Authors:  Lee-Ping Wang; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem Lett       Date:  2014-05-16       Impact factor: 6.475

2.  The bend angle of water in ice Ih and liquid water: The significance of implementing the nonlinear monomer dipole moment surface in classical interaction potentials.

Authors:  George S Fanourgakis; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2006-05-07       Impact factor: 3.488

3.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

4.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

5.  Current status of the AMOEBA polarizable force field.

Authors:  Jay W Ponder; Chuanjie Wu; Pengyu Ren; Vijay S Pande; John D Chodera; Michael J Schnieders; Imran Haque; David L Mobley; Daniel S Lambrecht; Robert A DiStasio; Martin Head-Gordon; Gary N I Clark; Margaret E Johnson; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

6.  Systematic improvement of a classical molecular model of water.

Authors:  Lee-Ping Wang; Teresa Head-Gordon; Jay W Ponder; Pengyu Ren; John D Chodera; Peter K Eastman; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem B       Date:  2013-08-14       Impact factor: 2.991

7.  General van der Waals potential for common organic molecules.

Authors:  Rui Qi; Qiantao Wang; Pengyu Ren
Journal:  Bioorg Med Chem       Date:  2016-08-02       Impact factor: 3.641

8.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Authors:  Peter Eastman; Jason Swails; John D Chodera; Robert T McGibbon; Yutong Zhao; Kyle A Beauchamp; Lee-Ping Wang; Andrew C Simmonett; Matthew P Harrigan; Chaya D Stern; Rafal P Wiewiora; Bernard R Brooks; Vijay S Pande
Journal:  PLoS Comput Biol       Date:  2017-07-26       Impact factor: 4.475

9.  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

10.  A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics.

Authors:  Zak E Hughes; Emmanuel Ren; Joseph C R Thacker; Benjamin C B Symons; Arnaldo F Silva; Paul L A Popelier
Journal:  J Comput Chem       Date:  2019-11-20       Impact factor: 3.376

View more
  12 in total

1.  Driving torsion scans with wavefront propagation.

Authors:  Yudong Qiu; Daniel G A Smith; Chaya D Stern; Mudong Feng; Hyesu Jang; Lee-Ping Wang
Journal:  J Chem Phys       Date:  2020-06-28       Impact factor: 3.488

2.  Atomic Polarizabilities for Interactive Dipole Induction Models.

Authors:  Jacob M Litman; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-12-28       Impact factor: 4.956

3.  Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics.

Authors:  Xudong Yang; Chengwen Liu; Brandon D Walker; Pengyu Ren
Journal:  J Chem Phys       Date:  2020-08-14       Impact factor: 3.488

4.  Automation of AMOEBA polarizable force field for small molecules: Poltype 2.

Authors:  Brandon Walker; Chengwen Liu; Elizabeth Wait; Pengyu Ren
Journal:  J Comput Chem       Date:  2022-07-01       Impact factor: 3.672

5.  Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.

Authors:  Rae A Corrigan; Guowei Qi; Andrew C Thiel; Jack R Lynn; Brandon D Walker; Thomas L Casavant; Louis Lagardere; Jean-Philip Piquemal; Jay W Ponder; Pengyu Ren; Michael J Schnieders
Journal:  J Chem Theory Comput       Date:  2021-03-26       Impact factor: 6.006

6.  Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case.

Authors:  Jacek Kozuch; Samuel H Schneider; Chu Zheng; Zhe Ji; Richard T Bradshaw; Steven G Boxer
Journal:  J Phys Chem B       Date:  2021-04-26       Impact factor: 2.991

7.  AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.

Authors:  Yuanjun Shi; Marie L Laury; Zhi Wang; Jay W Ponder
Journal:  J Comput Aided Mol Des       Date:  2020-11-03       Impact factor: 3.686

8.  Polarizable Water Potential Derived from a Model Electron Density.

Authors:  Joshua A Rackers; Roseane R Silva; Zhi Wang; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2021-10-26       Impact factor: 6.006

9.  Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.

Authors:  Zhifeng Jing; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-06-07       Impact factor: 6.162

10.  Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems.

Authors:  Olivier Adjoua; Louis Lagardère; Luc-Henri Jolly; Arnaud Durocher; Thibaut Very; Isabelle Dupays; Zhi Wang; Théo Jaffrelot Inizan; Frédéric Célerse; Pengyu Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2021-03-23       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.