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QUASAR: A Flexible QM-MM Method for Biomolecular Systems based on Restraining Spheres

  • Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as nuclear quantum effects. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system.

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Metadaten
Author:Christoph Gorgulla, Alejandro J. Garza, Venkat Kapil, Konstantin Fackeldey
Document Type:Article
Parent Title (English):Computer Physics Communications
Tag:Binding; CADD; Free Energy; Path Integral; QM-MM Methods; biomolecular systems
Date of first Publication:2025/11/17
ISSN:0010-4655
DOI:https://doi.org/10.1016/j.cpc.2025.109949
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