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Pré-Publication, Document De Travail Année : 2022

An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators

Résumé

Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their applicability. In the literature, several works have attempted to define a QM/MM model in periodic boundary conditions (PBC) but frequently the models are too time-consuming for general applicability to biological systems in solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC combining the benefits of electrostatic potential fitted (ESPF) atomic charges and particle-mesh Ewald sums, that can efficiently treat systems of arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for arabidopsis thaliana cryptochrome 1 containing circa 93000 atoms, reproducing accurately the experimental absorption maximum

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Dates et versions

hal-03846131 , version 1 (10-11-2022)

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  • HAL Id : hal-03846131 , version 1

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Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant. An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators. 2022. ⟨hal-03846131⟩
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