MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC
MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field pa...
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| Veröffentlicht in: | Journal of chemical information and modeling 2023-02, Vol.63 (4), p.1218-1228 |
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| container_title | Journal of chemical information and modeling |
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| creator | Crawford, Brad Timalsina, Umesh Quach, Co D Craven, Nicholas C Gilmer, Justin B McCabe, Clare Cummings, Peter T Potoff, Jeffrey J |
| description | MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO
in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC. |
| doi_str_mv | 10.1021/acs.jcim.2c01498 |
| format | Article |
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in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.</description><identifier>ISSN: 1549-9596</identifier><identifier>EISSN: 1549-960X</identifier><identifier>DOI: 10.1021/acs.jcim.2c01498</identifier><identifier>PMID: 36791286</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Data analysis ; Jet engine fuels ; Neon ; Parameters ; Simulation ; Software ; Workflow</subject><ispartof>Journal of chemical information and modeling, 2023-02, Vol.63 (4), p.1218-1228</ispartof><rights>Copyright American Chemical Society Feb 27, 2023</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c327t-e29615f91db64ab6e1d806356bb114d0d841ec90e98061150713c1da58d124303</citedby><cites>FETCH-LOGICAL-c327t-e29615f91db64ab6e1d806356bb114d0d841ec90e98061150713c1da58d124303</cites><orcidid>0000-0002-4421-8787 ; 0000-0002-8552-9135 ; 0000-0003-0638-7333</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,2765,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36791286$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Crawford, Brad</creatorcontrib><creatorcontrib>Timalsina, Umesh</creatorcontrib><creatorcontrib>Quach, Co D</creatorcontrib><creatorcontrib>Craven, Nicholas C</creatorcontrib><creatorcontrib>Gilmer, Justin B</creatorcontrib><creatorcontrib>McCabe, Clare</creatorcontrib><creatorcontrib>Cummings, Peter T</creatorcontrib><creatorcontrib>Potoff, Jeffrey J</creatorcontrib><title>MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC</title><title>Journal of chemical information and modeling</title><addtitle>J Chem Inf Model</addtitle><description>MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO
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| language | eng |
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| source | ACS Publications |
| subjects | Data analysis Jet engine fuels Neon Parameters Simulation Software Workflow |
| title | MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC |
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