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Creators/Authors contains: "Faraji, Shirin"

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Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase

https://doi.org/10.1021/acs.jpca.3c03546

Menger, Maximilian_F_S J; Ou, Qi; Shao, Yihan; Faraji, Shirin; Subotnik, Joseph E; Cofer-Shabica, D Vale (October 2023, The Journal of Physical Chemistry A)

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Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

https://doi.org/10.1021/jacs.3c02229

Grigorenko, Bella L; Polyakov, Igor V; Khrenova, Maria G; Giudetti, Goran; Faraji, Shirin; Krylov, Anna I; Nemukhin, Alexander V (June 2023, Journal of the American Chemical Society)

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M-Chem: a modular software package for molecular simulation that spans scientific domains

https://doi.org/10.1080/00268976.2022.2129500

Witek, Jagna; Heindel, Joseph P.; Guan, Xingyi; Leven, Itai; Hao, Hongxia; Naullage, Pavithra; LaCour, Allen; Sami, Selim; Menger, M. F.; Cofer-Shabica, D. Vale; et al (October 2023, Molecular Physics)

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How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

https://doi.org/10.1021/acs.jctc.2c00286

Giudetti, Goran; Polyakov, Igor; Grigorenko, Bella L.; Faraji, Shirin; Nemukhin, Alexander V.; Krylov, Anna I. (August 2022, Journal of Chemical Theory and Computation)

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INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations

https://doi.org/10.1021/acs.jctc.2c00204

Cofer-Shabica, D. Vale; Menger, Maximilian F.; Ou, Qi; Shao, Yihan; Subotnik, Joseph E.; Faraji, Shirin (July 2022, Journal of Chemical Theory and Computation)

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Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

https://doi.org/10.1063/5.0055522

Epifanovsky, Evgeny; Gilbert, Andrew T.; Feng, Xintian; Lee, Joonho; Mao, Yuezhi; Mardirossian, Narbe; Pokhilko, Pavel; White, Alec F.; Coons, Marc P.; Dempwolff, Adrian L.; et al (August 2021, The Journal of Chemical Physics)

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