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ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale

W F Drew Bennett1, Austen Bernardi1, Tugba Nur Ozturk1

  • 1Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

Molecules (Basel, Switzerland)
|August 10, 2024
PubMed
Summary
This summary is machine-generated.

ezAlign software converts coarse-grained molecular dynamics structures to atomistic representation. This enables multiscale modeling for complex biological systems, bridging disparate time and length scales.

Keywords:
molecular dynamicsmultiscale modelingsoftware

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Area of Science:

  • Computational physics and chemistry
  • Biomolecular modeling
  • Soft condensed matter physics

Background:

  • Studying soft condensed matter and biomolecular systems is hindered by vast, disparate time and length scales.
  • Accurate representation of complex systems requires multiscale simulations.
  • Bridging these scales is crucial for understanding biological processes.

Purpose of the Study:

  • To introduce ezAlign, an open-source software for converting coarse-grained molecular dynamics (MD) structures to atomistic representation.
  • To facilitate multiscale modeling of biomolecular systems by enabling seamless integration of different simulation scales.
  • To provide a user-friendly tool and comprehensive examples for researchers.

Main Methods:

  • ezAlign employs a methodology based on aligning an atomistic template molecule to a coarse-grained structure.
  • Position-restraint energy minimization is used to ensure the atomistic molecule adopts a conformation consistent with the coarse-grained representation.
  • The process involves combining, solvating, minimizing, and equilibrating molecules with position restraints.

Main Results:

  • Validation was performed on a pure POPC membrane, comparing ezAlign with other popular membrane construction methods.
  • Demonstrated successful application to diverse systems including surfactant self-assembly, membrane proteins, and complex bacterial and human plasma membrane models.
  • The ezAlign v1.1 software package is publicly available with supporting examples and parameter files.

Conclusions:

  • ezAlign effectively converts coarse-grained MD structures to atomistic representation, enabling multiscale modeling.
  • The software and provided resources simplify the construction of complex biomolecular systems for simulation.
  • This work significantly aids future multiscale modeling efforts in biology and soft matter physics.