Literature DB >> 35317572

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.

Haixin Wei1, Piotr Cieplak2, Yong Duan3, Ray Luo1.   

Abstract

Our previous article has established the theory of molecular dynamics (MD) simulations for systems modeled with the polarizable Gaussian multipole (pGM) electrostatics [Wei et al., J. Chem. Phys. 153(11), 114116 (2020)]. Specifically, we proposed the covalent basis vector framework to define the permanent multipoles and derived closed-form energy and force expressions to facilitate an efficient implementation of pGM electrostatics. In this study, we move forward to derive the pGM internal stress tensor for constant pressure MD simulations with the pGM electrostatics. Three different formulations are presented for the flexible, rigid, and short-range screened systems, respectively. The analytical formulations were implemented in the SANDER program in the Amber package and were first validated with the finite-difference method for two different boxes of pGM water molecules. This is followed by a constant temperature and constant pressure MD simulation for a box of 512 pGM water molecules. Our results show that the simulation system stabilized at a physically reasonable state and maintained the balance with the externally applied pressure. In addition, several fundamental differences were observed between the pGM and classic point charge models in terms of the simulation behaviors, indicating more extensive parameterization is necessary to utilize the pGM electrostatics.

Entities:  

Year:  2022        PMID: 35317572      PMCID: PMC9088672          DOI: 10.1063/5.0082548

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

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Journal:  Curr Opin Struct Biol       Date:  2001-04       Impact factor: 6.809

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Journal:  Adv Protein Chem       Date:  2003

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

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Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

5.  Tinker 8: Software Tools for Molecular Design.

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Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

6.  Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy.

Authors:  Junmei Wang; Piotr Cieplak; Ray Luo; Yong Duan
Journal:  J Chem Theory Comput       Date:  2019-02-04       Impact factor: 6.006

7.  Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.

Authors:  Celeste Sagui; Lee G Pedersen; Thomas A Darden
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

  7 in total
  1 in total

1.  PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields.

Authors:  Shiji Zhao; Haixin Wei; Piotr Cieplak; Yong Duan; Ray Luo
Journal:  J Chem Theory Comput       Date:  2022-05-10       Impact factor: 6.578

  1 in total

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