PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software
Abstract PyGAMD (Python GPU‐accelerated molecular dynamics software) is a molecular simulation platform developed from scratch. It is designed for soft matter, especially for polymer by integrating coarse‐grained/multi‐scale models, methods, and force fields. It essentially includes an interpreter o...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley-VCH
2025-06-01
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| Series: | Materials Genome Engineering Advances |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/mgea.70019 |
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| _version_ | 1849320648618278912 |
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| author | Jialei Xu Shenghong Guo Miaolan Zhen Zhuochen Yu Youliang Zhu Giuseppe Milano Zhongyuan Lu |
| author_facet | Jialei Xu Shenghong Guo Miaolan Zhen Zhuochen Yu Youliang Zhu Giuseppe Milano Zhongyuan Lu |
| author_sort | Jialei Xu |
| collection | DOAJ |
| description | Abstract PyGAMD (Python GPU‐accelerated molecular dynamics software) is a molecular simulation platform developed from scratch. It is designed for soft matter, especially for polymer by integrating coarse‐grained/multi‐scale models, methods, and force fields. It essentially includes an interpreter of molecular dynamics (MD) which supports secondary programming so that users can write their own functions by themselves, such as analytical potential forms for nonbonded, bond, angle, and dihedral interactions in an easy way, greatly extending the flexibility of MD simulations. The interpreter is written by pure Python language, making it easy to be modified and further developed. Some built‐in libraries written by other languages that have been compiled for Python are added into PyGAMD to extend it's features, including configuration initialization, property analysis, etc. Machine learning force fields that are trained by DeePMD‐kit are supported by PyGAMD for conveniently implementing multi‐scale modeling and simulations. By designing an advanced framework of software, graphics processing unit‐acceleration achieved by the Numba library of Python and compute unified device architecture reaches a high computing efficiency. |
| format | Article |
| id | doaj-art-89e59be1c9d34ef8b39c12916680b8b1 |
| institution | Kabale University |
| issn | 2940-9489 2940-9497 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley-VCH |
| record_format | Article |
| series | Materials Genome Engineering Advances |
| spelling | doaj-art-89e59be1c9d34ef8b39c12916680b8b12025-08-20T03:50:00ZengWiley-VCHMaterials Genome Engineering Advances2940-94892940-94972025-06-0132n/an/a10.1002/mgea.70019PyGAMD: Python graphics processing unit‐accelerated molecular dynamics softwareJialei Xu0Shenghong Guo1Miaolan Zhen2Zhuochen Yu3Youliang Zhu4Giuseppe Milano5Zhongyuan Lu6State Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaState Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaState Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaState Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaState Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaDepartment of Chemical, Materials and Production Engineering University of Naples Federico II Napoli ItalyState Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun ChinaAbstract PyGAMD (Python GPU‐accelerated molecular dynamics software) is a molecular simulation platform developed from scratch. It is designed for soft matter, especially for polymer by integrating coarse‐grained/multi‐scale models, methods, and force fields. It essentially includes an interpreter of molecular dynamics (MD) which supports secondary programming so that users can write their own functions by themselves, such as analytical potential forms for nonbonded, bond, angle, and dihedral interactions in an easy way, greatly extending the flexibility of MD simulations. The interpreter is written by pure Python language, making it easy to be modified and further developed. Some built‐in libraries written by other languages that have been compiled for Python are added into PyGAMD to extend it's features, including configuration initialization, property analysis, etc. Machine learning force fields that are trained by DeePMD‐kit are supported by PyGAMD for conveniently implementing multi‐scale modeling and simulations. By designing an advanced framework of software, graphics processing unit‐acceleration achieved by the Numba library of Python and compute unified device architecture reaches a high computing efficiency.https://doi.org/10.1002/mgea.70019GPU‐accelerationinterpretermolecular dynamicsmulti‐scalepolymersoft matter |
| spellingShingle | Jialei Xu Shenghong Guo Miaolan Zhen Zhuochen Yu Youliang Zhu Giuseppe Milano Zhongyuan Lu PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software Materials Genome Engineering Advances GPU‐acceleration interpreter molecular dynamics multi‐scale polymer soft matter |
| title | PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software |
| title_full | PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software |
| title_fullStr | PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software |
| title_full_unstemmed | PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software |
| title_short | PyGAMD: Python graphics processing unit‐accelerated molecular dynamics software |
| title_sort | pygamd python graphics processing unit accelerated molecular dynamics software |
| topic | GPU‐acceleration interpreter molecular dynamics multi‐scale polymer soft matter |
| url | https://doi.org/10.1002/mgea.70019 |
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