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Article Dans Une Revue Zeitschrift fur Naturforschung B Année : 2024

A molecular mechanics implementation of the cyclic cluster model

Résumé

Abstract The implementation of the cyclic cluster model (CCM) for molecular mechanics is presented in the framework of the computational chemistry program deMon 2 k . Because the CCM is particularly well-suited for the description of periodic systems with defects, it can be used for periodic QM/MM approaches where the non-periodic QM part is treated as a defect in a periodic MM surrounding. To this end, we present here the explicit formulae for the evaluation of the Ewald sum and its first- and second-order derivatives as implemented in deMon 2 k . The outlined implementation was tested in molecular dynamics (MD) simulations and periodic structure optimization calculations. MD simulations of an argon system were carried out using the Nosé-Hoover chain (NHC) thermostat and the Martyna-Tobias-Klein (MTK) barostat to control the temperature and pressure of the system, respectively. For the validation of CCM structure optimization a set of molecular crystals were optimized using the Ewald method for the evaluation of the electrostatic interactions. Two optimization procedures for the determination of the atomic positions and CCM cell parameters were tested. Our results show that the simultaneous optimization of the atomic positions and cell parameters is most efficient.

Domaines

Chimie

Dates et versions

hal-04567111 , version 1 (03-05-2024)

Identifiants

Citer

Juan Diego Samaniego-Rojas, Robin Gaumard, José Alejandre, Tzonka Mineva, Gerald Geudtner, et al.. A molecular mechanics implementation of the cyclic cluster model. Zeitschrift fur Naturforschung B, 2024, 79 (4), pp.201-213. ⟨10.1515/znb-2023-0090⟩. ⟨hal-04567111⟩
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