Amber free energy tools : Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials
Tao, Yujun and Giese, Timothy J. and Ekesan, Şölen and Zeng, Jinzhe and Aradi, Bálint and Hourahine, Ben and Aktulga, Hasan Metin and Götz, Andreas W. and Merz, Kenneth M. and York, Darrin M. (2024) Amber free energy tools : Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials. Journal of Chemical Physics, 160 (22). 224104. ISSN 0021-9606 (https://doi.org/10.1063/5.0211276)
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Abstract
We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform “system calls” and enable the incorporation of long-range Ewald electrostatics into the external software’s self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM–ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client–server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM–ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.
ORCID iDs
Tao, Yujun, Giese, Timothy J., Ekesan, Şölen, Zeng, Jinzhe, Aradi, Bálint, Hourahine, Ben ORCID: https://orcid.org/0000-0002-7667-7101, Aktulga, Hasan Metin, Götz, Andreas W., Merz, Kenneth M. and York, Darrin M.;-
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Item type: Article ID code: 89682 Dates: DateEvent14 June 2024Published10 June 2024Published Online15 May 2024Accepted29 March 2024SubmittedSubjects: Science > Mathematics > Computer software
Science > PhysicsDepartment: Strategic Research Themes > Measurement Science and Enabling Technologies
Faculty of Science > PhysicsDepositing user: Pure Administrator Date deposited: 21 Jun 2024 08:59 Last modified: 25 Sep 2024 14:57 Related URLs: URI: https://strathprints.strath.ac.uk/id/eprint/89682