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CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.

Yeol Kyo Choi1, Nathan R Kern2, Seonghan Kim3

  • 1Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.

Journal of Chemical Theory and Computation
|December 6, 2021
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Summary

Nanomaterial Modeler in CHARMM-GUI automates the creation of nanomaterial models for molecular dynamics simulations. This tool enhances the study of nanomaterials by providing reliable force fields and validated parameters for diverse applications.

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Area of Science:

  • Computational Nanoscience
  • Materials Science
  • Molecular Dynamics

Background:

  • Molecular modeling and simulation are crucial for predicting nanomaterial properties.
  • Building complex nanomaterial systems for simulations is currently challenging due to limited cyberinfrastructure.

Purpose of the Study:

  • To introduce Nanomaterial Modeler, a web-based cyberinfrastructure within CHARMM-GUI.
  • To provide an automated workflow for generating nanomaterial models, topologies, and simulation files.

Main Methods:

  • Utilized the interface force field for nanomaterial models.
  • Assessed model transferability using single-point energy calculations.
  • Validated Lennard-Jones (LJ) cutoff methods (12 cutoff, 10-12 fsw, LJPME) for compatibility with biomolecular force fields.
  • Generated complex nanomaterial-biomolecule and nanomaterial-polymer interfaces.

Main Results:

  • Achieved 0.01% relative absolute energy differences in transferability assessments.
  • Demonstrated good agreement between computed and experimental density and surface energies.
  • Observed varying simulation results based on LJ cutoff methods: 10-12 fsw < 12 cutoff < LJPME.
  • Reported up to 4% deviation in density and 8% in surface energy for LJ-dominant nanomaterials.

Conclusions:

  • Nanomaterial Modeler offers a reliable and automated solution for simulating nanomaterial systems.
  • The tool supports state-of-the-art molecular dynamics simulations across various packages.
  • It facilitates innovative research into the structure, dynamics, and mechanisms of complex nanomaterial-containing systems.