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DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields.

Carlos E S Bernardes1

  • 1Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.

Journal of Chemical Information and Modeling
|March 3, 2022
PubMed
Summary
This summary is machine-generated.

DLPGEN simplifies molecular dynamics (MD) simulations by generating input files for multiple programs, including support for polarizable force fields. This tool ensures accurate results for systems like liquid ethanol across different simulation packages.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Materials Science

Background:

  • Preparing input files for molecular dynamics (MD) simulations is complex and time-consuming.
  • Existing file conversion tools often have limitations with force field support, especially for polarization models.

Purpose of the Study:

  • To introduce DLPGEN, a novel program for generating input files for multiple MD simulation packages.
  • To enable the preparation of polarizable force fields for simulations.

Main Methods:

  • DLPGEN generates input files for GROMACS, CHARMM, DL_POLY, and LAMMPS.
  • It supports polarizable force fields via self-consistent field or dual thermostat-extended Lagrangian approaches.
  • A new polarization scheme for GROMACS with multiple virtual particles is presented.

Main Results:

  • Simulations of liquid ethanol using DLPGEN-generated files showed good agreement in configurational energy, density, and diffusion coefficients between GROMACS, LAMMPS, and CHARMM.
  • DL_POLY encountered issues with Shells temperature control for systems with multiple Drude particles.

Conclusions:

  • DLPGEN is a versatile tool for creating MD input files, facilitating the use of polarizable force fields across various simulation platforms.
  • The program enhances the accuracy and compatibility of MD simulations, though potential limitations with specific programs like DL_POLY for certain systems should be noted.