Accurate QM/MM Molecular Dynamics for Periodic Systems in \textsc{GPU4PySCF} with Applications to Enzyme Catalysis
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arXiv
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866917845711978496 |
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| author | Li, Chenghan Chan, Garnet Kin-Lic |
| author_facet | Li, Chenghan Chan, Garnet Kin-Lic |
| contents | We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the QM/MM boundary. We demonstrate that our method has well-controlled errors, stable self-consistent QM convergence, and energy-conserving dynamics. We further describe an application to the catalytic kinetics of chorismate mutase. Using an accurate hybrid functional reparametrized to coupled cluster energetics, our QM/MM simulations highlight the sensitivity in the calculated rate to the choice of quantum method, quantum region selection, and local protein conformation. Our work is provided through the open-source \textsc{PySCF} package using acceleration from the \textsc{GPU4PySCF} module. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2408_03273 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Accurate QM/MM Molecular Dynamics for Periodic Systems in \textsc{GPU4PySCF} with Applications to Enzyme Catalysis Li, Chenghan Chan, Garnet Kin-Lic Chemical Physics Biological Physics We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the QM/MM boundary. We demonstrate that our method has well-controlled errors, stable self-consistent QM convergence, and energy-conserving dynamics. We further describe an application to the catalytic kinetics of chorismate mutase. Using an accurate hybrid functional reparametrized to coupled cluster energetics, our QM/MM simulations highlight the sensitivity in the calculated rate to the choice of quantum method, quantum region selection, and local protein conformation. Our work is provided through the open-source \textsc{PySCF} package using acceleration from the \textsc{GPU4PySCF} module. |
| title | Accurate QM/MM Molecular Dynamics for Periodic Systems in \textsc{GPU4PySCF} with Applications to Enzyme Catalysis |
| topic | Chemical Physics Biological Physics |
| url | https://arxiv.org/abs/2408.03273 |