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LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Eric G Kratz1, Alice R Walker1, Louis Lagardère2,3

  • 1Department of Chemistry, Wayne State University, Detroit, Michigan, 48202.

Journal of Computational Chemistry
|January 20, 2016
PubMed
Summary
This summary is machine-generated.

The new LICHEM software enables quantum mechanics/molecular mechanics (QM/MM) calculations with polarizable force fields, improving accuracy for molecular simulations by including explicit polarization effects.

Keywords:
AMOEBAQM/MMmultipolespolarizationpseudo-bond

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Accurate molecular simulations require sophisticated methods to model complex systems.
  • Quantum mechanics/molecular mechanics (QM/MM) is a powerful approach for studying large systems by combining quantum and classical mechanics.
  • Polarizable force fields are crucial for capturing the electronic response of molecules, which is vital for many chemical and biological processes.

Purpose of the Study:

  • To introduce and validate the initial implementation of the LICHEM software package.
  • To enable seamless integration of quantum mechanics (QM) and molecular mechanics (MM) calculations with polarizable force fields.
  • To demonstrate the utility of LICHEM for various computational chemistry tasks.

Main Methods:

  • LICHEM interfaces with established QM (Gaussian, PSI4, NWChem) and MM (TINKER, TINKER-HP) packages.
  • The software extracts forces and energies from unmodified QM and MM packages for calculations.
  • A pseudo-bond approach is used for smooth QM/MM transitions across covalent bonds, incorporating polarizable force fields.

Main Results:

  • The LICHEM software package has been successfully implemented and tested.
  • Calculations on water clusters and small peptides demonstrate the software's capabilities.
  • Results highlight the significant impact of explicit polarization on simulation accuracy.

Conclusions:

  • LICHEM provides a versatile platform for QM/MM calculations utilizing polarizable force fields.
  • The software facilitates geometry optimizations, single-point energy calculations, and Monte Carlo simulations.
  • The inclusion of explicit polarization is essential for reliable molecular modeling, as shown by the study's findings.