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Polymer Builder Extension for MosDef-mBuild: mbuild_polybuild
When modeling polymers in simulations, building a simulation box is a consistent barrier. Although many tools now exist for that purpose, not one contains all features that one would desire. A more specific failing is the handling of the polymer tacticity. MosDef's mBuild [DOI: 10.1007/978-981-10-1128-3_5] offers the flexibility to account for this important aspect of polymer structure, although not readily. This package contains mBuild "recipies" for common polymer backbone chemistries as well as common functional groups. The numerous chemistries supported are made available through a script to import .pdb files as chemistries, where some atom names can be chosen to represent a mBuild `Port` for further flexibility in connecting several functional groups. In addition, the chemistries supported in this package are accompanied by a MosDef-foyer [DOI: 10.1016/j.commatsci.2019.05.026] forcefield file for OPLS-AA with expanded atom definitions and typing to accommodate.
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| accrualPeriodicity | R/P6M |
| bureauCode |
[ "006:55" ] |
| contactPoint |
{ "fn": "Debra Audus", "hasEmail": "mailto:debra.audus@nist.gov" } |
| description | When modeling polymers in simulations, building a simulation box is a consistent barrier. Although many tools now exist for that purpose, not one contains all features that one would desire. A more specific failing is the handling of the polymer tacticity. MosDef's mBuild [DOI: 10.1007/978-981-10-1128-3_5] offers the flexibility to account for this important aspect of polymer structure, although not readily. This package contains mBuild "recipies" for common polymer backbone chemistries as well as common functional groups. The numerous chemistries supported are made available through a script to import .pdb files as chemistries, where some atom names can be chosen to represent a mBuild `Port` for further flexibility in connecting several functional groups. In addition, the chemistries supported in this package are accompanied by a MosDef-foyer [DOI: 10.1016/j.commatsci.2019.05.026] forcefield file for OPLS-AA with expanded atom definitions and typing to accommodate. |
| distribution |
[ { "title": "GitHub Link", "format": "This code is hosted on GitHub in a repository.", "accessURL": "https://github.com/usnistgov/mbuild_polybuild", "description": "This is a link to the GitHub repository where the package, mbuild_package, is hosted." } ] |
| identifier | ark:/88434/mds2-3640 |
| issued | 2025-08-20 |
| keyword |
[ "molecular dynamics", "polymers", "simulations" ] |
| landingPage | https://data.nist.gov/od/id/mds2-3640 |
| language |
[ "en" ] |
| license | https://www.nist.gov/open/license |
| modified | 2024-11-19 00:00:00 |
| programCode |
[ "006:045" ] |
| publisher |
{ "name": "National Institute of Standards and Technology", "@type": "org:Organization" } |
| theme |
[ "Chemistry:Theoretical chemistry and modeling" ] |
| title | Polymer Builder Extension for MosDef-mBuild: mbuild_polybuild |
