PMID- 37791670
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231020
IS  - 1520-5207 (Electronic)
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 127
IP  - 40
DP  - 2023 Oct 12
TI  - OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.
PG  - 8537-8550
LID - 10.1021/acs.jpcb.3c04473 [doi]
AB  - 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.
FAU - Peng, Yuxing
AU  - Peng Y
AD  - NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, California 95051, 
      United States.
FAU - Pak, Alexander J
AU  - Pak AJ
AD  - Department of Chemical and Biological Engineering, Colorado School of Mines, 
      Golden, Colorado 80401, United States.
FAU - Durumeric, Aleksander E P
AU  - Durumeric AEP
AD  - Department of Mathematics and Computer Science, Freie Universitat Berlin, Berlin 
      14195, Germany.
FAU - Sahrmann, Patrick G
AU  - Sahrmann PG
AUID- ORCID: 0000-0002-4781-9561
AD  - 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.
FAU - Mani, Sriramvignesh
AU  - Mani S
AD  - 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.
FAU - Jin, Jaehyeok
AU  - Jin J
AUID- ORCID: 0000-0003-3859-3545
AD  - 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.
FAU - Loose, Timothy D
AU  - Loose TD
AD  - 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.
FAU - Beiter, Jeriann
AU  - Beiter J
AD  - 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.
FAU - Voth, Gregory A
AU  - Voth GA
AUID- ORCID: 0000-0002-3267-6748
AD  - 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.
LA  - eng
PT  - Journal Article
DEP - 20231004
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
SB  - IM
PMC - PMC10577682
COIS- The authors declare no competing financial interest.
EDAT- 2023/10/04 12:45
MHDA- 2023/10/04 12:46
PMCR- 2023/10/16
CRDT- 2023/10/04 08:03
PHST- 2023/10/04 12:46 [medline]
PHST- 2023/10/04 12:45 [pubmed]
PHST- 2023/10/04 08:03 [entrez]
PHST- 2023/10/16 00:00 [pmc-release]
AID - 10.1021/acs.jpcb.3c04473 [doi]
PST - ppublish
SO  - J Phys Chem B. 2023 Oct 12;127(40):8537-8550. doi: 10.1021/acs.jpcb.3c04473. Epub 
      2023 Oct 4.