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Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

Software ·
DOI:https://doi.org/10.11578/dc.20250307.10· OSTI ID:code-152512 · Code ID:152512
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We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Short Name / Acronym:
iMMD
Site Accession Number:
O4782
Software Type:
Scientific
License(s):
MIT License
Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
NATIONAL Institue of Health
Primary Award/Contract Number:
AC52-06NA25396
DOE Contract Number:
AC52-06NA25396
Code ID:
152512
OSTI ID:
code-152512
Country of Origin:
United States

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