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CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems

Author

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  • Nathan R. Kern

    (Lehigh University)

  • Jumin Lee

    (Lehigh University)

  • Yeol Kyo Choi

    (Lehigh University)

  • Wonpil Im

    (Lehigh University
    Lehigh University
    Lehigh University)

Abstract

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.

Suggested Citation

  • Nathan R. Kern & Jumin Lee & Yeol Kyo Choi & Wonpil Im, 2024. "CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49700-4
    DOI: 10.1038/s41467-024-49700-4
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    3. Yasushi Shibuta & Shinji Sakane & Eisuke Miyoshi & Shin Okita & Tomohiro Takaki & Munekazu Ohno, 2017. "Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal," Nature Communications, Nature, vol. 8(1), pages 1-9, December.
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