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OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining. | LitMetric

OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.

J Phys Chem B

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.

Published: October 2023

AI Article Synopsis

  • The "bottom-up" approach in computational modeling, particularly in fields like chemistry, biophysics, and materials science, focuses on creating simplified models from detailed simulations for analyzing complex systems.
  • The Multiscale Coarse-Graining (MS-CG) technique allows for the accurate derivation of these models using data from fine-grained simulations, enhancing efficiency and accuracy.
  • OpenMSCG is a new open-source software that offers various bottom-up CG methods and enables customization and reproducibility in modeling, making it easier for researchers to derive coarse-grained models from molecular dynamics data.

Article Abstract

The "bottom-up" approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling "recipes" for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10577682PMC
http://dx.doi.org/10.1021/acs.jpcb.3c04473DOI Listing

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