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OpenMM-Python-Force: Deploying Accelerated Python Modules in Molecular Dynamics Simulation

Guardat en:
Publicat a:arXiv.org (Dec 24, 2024), p. n/a
Autor principal: Wang, Zhi
Altres autors: Wen, Yan
Publicat:
Cornell University Library, arXiv.org
Matèries:
Python
Source code
Modules
Data exchange
Molecular dynamics
Tensors
Accés en línia:Citation/Abstract
Full text outside of ProQuest
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022 |a 2331-8422 
035 |a 3149108656 
045 0 |b d20241224 
100 1 |a Wang, Zhi 
245 1 |a OpenMM-Python-Force: Deploying Accelerated Python Modules in Molecular Dynamics Simulation 
260 |b Cornell University Library, arXiv.org  |c Dec 24, 2024 
513 |a Working Paper 
520 3 |a We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data exchange can be implemented through torch.Tensor or numpy.ndarray, depending on the specific use case. This enhancement significantly expands OpenMM's capabilities, facilitating seamless integration of accelerated Python modules within molecular dynamics simulations. This approach represents a general solution that can be adapted to other molecular dynamics engines beyond OpenMM. The source code is openly available at https://github.com/bytedance/OpenMM-Python-Force. 
653 |a Python 
653 |a Source code 
653 |a Modules 
653 |a Data exchange 
653 |a Molecular dynamics 
653 |a Tensors 
700 1 |a Wen, Yan 
773 0 |t arXiv.org  |g (Dec 24, 2024), p. n/a 
786 0 |d ProQuest  |t Engineering Database 
856 4 1 |3 Citation/Abstract  |u https://www.proquest.com/docview/3149108656/abstract/embedded/6A8EOT78XXH2IG52?source=fedsrch 
856 4 0 |3 Full text outside of ProQuest  |u http://arxiv.org/abs/2412.18271