HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers
Generation of realistic all-atom configurations of crosslinked polymer systems is a difficult task which so far has mainly been tackled using either closed-source software or bespoke, highly user-intensive efforts. In this work, we present a robust, open-source Python package HTPolyNet designed to g...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-02-01
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| Series: | SoftwareX |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711022002217 |
| _version_ | 1811166101609906176 |
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| author | Ming Huang Cameron F. Abrams |
| author_facet | Ming Huang Cameron F. Abrams |
| author_sort | Ming Huang |
| collection | DOAJ |
| description | Generation of realistic all-atom configurations of crosslinked polymer systems is a difficult task which so far has mainly been tackled using either closed-source software or bespoke, highly user-intensive efforts. In this work, we present a robust, open-source Python package HTPolyNet designed to generate polymerized and/or crosslinked all-atom systems using only input monomer structures and a description of the polymerization chemistry. HTPolyNet works with the popular GROMACS molecular dynamics package and the General Amber Force Field. In addition to describing the structure and usage of HTPolyNetwe also demonstrate its application to two distinct systems: a vinyl-ester based resin and an epoxy-amine resin, both of which form dense, amorphous network systems. |
| first_indexed | 2024-04-10T15:48:10Z |
| format | Article |
| id | doaj.art-162d9d8a5db84594be4db6d9597e28bc |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-04-10T15:48:10Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-162d9d8a5db84594be4db6d9597e28bc2023-02-12T04:15:10ZengElsevierSoftwareX2352-71102023-02-0121101303HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymersMing Huang0Cameron F. Abrams1Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, 19130, USACorresponding author.; Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, 19130, USAGeneration of realistic all-atom configurations of crosslinked polymer systems is a difficult task which so far has mainly been tackled using either closed-source software or bespoke, highly user-intensive efforts. In this work, we present a robust, open-source Python package HTPolyNet designed to generate polymerized and/or crosslinked all-atom systems using only input monomer structures and a description of the polymerization chemistry. HTPolyNet works with the popular GROMACS molecular dynamics package and the General Amber Force Field. In addition to describing the structure and usage of HTPolyNetwe also demonstrate its application to two distinct systems: a vinyl-ester based resin and an epoxy-amine resin, both of which form dense, amorphous network systems.http://www.sciencedirect.com/science/article/pii/S2352711022002217Network polymersMolecular simulationsTopology generation |
| spellingShingle | Ming Huang Cameron F. Abrams HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers SoftwareX Network polymers Molecular simulations Topology generation |
| title | HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers |
| title_full | HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers |
| title_fullStr | HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers |
| title_full_unstemmed | HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers |
| title_short | HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers |
| title_sort | htpolynet a general system generator for all atom molecular simulations of amorphous crosslinked polymers |
| topic | Network polymers Molecular simulations Topology generation |
| url | http://www.sciencedirect.com/science/article/pii/S2352711022002217 |
| work_keys_str_mv | AT minghuang htpolynetageneralsystemgeneratorforallatommolecularsimulationsofamorphouscrosslinkedpolymers AT cameronfabrams htpolynetageneralsystemgeneratorforallatommolecularsimulationsofamorphouscrosslinkedpolymers |