ArticleJournal of chemical theory and computation2023
PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- A Combined Experimental-Theoretical Approach Unveils the Comprehensive Asn Deamidation Kinetics.Journal of the American Chemical Society · 2026Article
- Microscopic basis of reaction center modulation in PsbA variants of photosystem II.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.Journal of molecular modeling · 2024Review
- Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations.Chemical science · 2024Article
- Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical-Computational Study.The journal of physical chemistry. B · 2023Article
- Unveiling the Excited State Dynamics of Indole in Solution.Journal of chemical theory and computation · 2023Article
- Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis.Molecules (Basel, Switzerland) · 2023Article
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Abstract
Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate.
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