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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.
Jakob, W.; Rhinelander, J.; Moldovan, D. Pybind11 – Seamless Operability between C++11 and Python. 2017; https://github.com/pybind/pybind11
2017
Earlier work this paper cites.
Lehtola, S.; Steigemann, C.; Oliveira, M. J.; Marques, M. A. Recent Developments in Libxc — A Comprehensive Library of Functionals for Density Functional Theory. SoftwareX 2018
2018
Earlier work this paper cites.
Rackers, J. A.; Wang, Z.; Lu, C.; Laury, M. L.; Lagardère, L.; Schnieders, M. J.; Piquemal, J.-P.; Ren, P.; Ponder, J. W. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation 2018
2018
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Sun, Q.; Zhang, X.; Banerjee, S.; Bao, P.; Barbry, M.; Blunt, N. S.; Bogdanov, N. A.; Booth, G. H.; Chen, J.; Cui, Z.-H.; Eriksen, J. J.; Gao, Y.; Guo, S.; Hermann, J.; Hermes, M. R.; Koh, K.; Koval, P.; Lehtola, S.; Li, Z.; Liu, J.; Mardirossian, N.; McClain, J. D.; Motta, M.; Mussard, B.; Pham, H. Q.; Pulkin, A.; Purwanto, W.; Robinson, P. J.; Ronca, E.; Sayfutyarova, E. R.; Scheurer, M.; Schurkus, H. F.; Smith, J. E. T.; Sun, C.; Sun, S.-N.; Upadhyay, S.; Wagner, L. K.; Wang, X.; White, A.; Whitfield, J. D.; Williamson, M. J.; Wouters, S.; Yang, J.; Yu, J. M.; Zhu, T.; Berkelbach, T. C.; Sharma, S.; Sokolov, A. Y.; Chan, G. K.-L. Recent Developments in the PySCF Program Package. The Journal of Chemical Physics 2020
2020
Earlier work this paper cites.
Thompson, A. P.; Aktulga, H. M.; Berger, R.; Bolintineanu, D. S.; Brown, W. M.; Crozier, P. S.; In ’T Veld, P. J.; Kohlmeyer, A.; Moore, S. G.; Nguyen, T. D.; Shan, R.; Stevens, M. J.; Tranchida, J.; Trott, C.; Plimpton, S. J. LAMMPS - a Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales. Computer Physics Communications 2022
2022
Cited alongside, same era.
Eastman, P.; Galvelis, R.; Peláez, R. P.; Abreu, C. R. A.; Farr, S. E.; Gallicchio, E.; Gorenko, A.; Henry, M. M.; Hu, F.; Huang, J.; Krämer, A.; Michel, J.; Mitchell, J. A.; Pande, V. S.; Rodrigues, J. P.; Rodriguez-Guerra, J.; Simmonett, A. C.; Singh, S.; Swails, J.; Turner, P.; Wang, Y.; Zhang, I.; Chodera, J. D.; De Fabritiis, G.; Markland, T. E. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry B 2024
2024
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2024
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2024
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2024
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Ansel, J.; Yang, E.; He, H.; Gimelshein, N.; Jain, A.; Voznesensky, M.; Bao, B.; Bell, P.; Berard, D.; Burovski, E.; Chauhan, G.; Chourdia, A.; Constable, W.; Desmaison, A.; DeVito, Z.; Ellison, E.; Feng, W.; Gong, J.; Gschwind, M.; Hirsh, B.; Huang, S.; Kalambarkar, K.; Kirsch, L.; Lazos, M.; Lezcano, M.; Liang, Y.; Liang, J.; Lu, Y.; Luk, C. K.; Maher, B.; Pan, Y.; Puhrsch, C.; Reso, M.; Saroufim, M.; Siraichi, M. Y.; Suk, H.; Zhang, S.; Suo, M.; Tillet, P.; Zhao, X.; Wang, E.; Zhou, K.; Zou, R.; Wang, X.; Mathews, A.; Wen, W.; Chanan, G.; Wu, P.; Chintala, S. PyTorch 2: Faster Machine Learning Through Dynamic Python Bytecode Transformation and Graph Compilation. Proceedings of the 29th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Volume 2. La Jolla CA USA, 2024; pp 929–947
2024
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Pelaez, R. P.; Simeon, G.; Galvelis, R.; Mirarchi, A.; Eastman, P.; Doerr, S.; Thölke, P.; Markland, T. E.; De Fabritiis, G. TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations. Journal of Chemical Theory and Computation 2024
2024
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OpenMM Torch. https://github.com/openmm/openmm-torch
Cited in the paper.
NNPOps. https://github.com/openmm/NNPOps
Cited in the paper.
SWIG. https://www.swig.org
Cited in the paper.
Wang, Z.; Ponder, J. W. Tinker9: Next Generation of Tinker with GPU Support. https://github.com/TinkerTools/tinker9
Cited in the paper.
Python/C API Reference Manual. https://docs.python.org/3/c-api/index.html
Cited in the paper.
Pybind11 Documentation: Embedding the Interpreter. https://pybind11.readthedocs.io/en/stable/advanced/embedding.html
Cited in the paper.