Efficient and Accurate Born-Oppenheimer Molecular Dynamics for Large Molecular Systems.
J Chem Theory Comput
; 13(11): 5479-5485, 2017 Nov 14.
Article
em En
| MEDLINE
| ID: mdl-29068678
An efficient scheme for the calculation of Born-Oppenheimer molecular dynamics (BOMD) simulations is introduced. It combines the corrected small basis set Hartree-Fock (HF-3c) method by Sure and Grimme [J. Comput. Chem. 2013, 43, 1672], extended Lagrangian BOMD (XL-BOMD) by Niklasson et al. [J. Chem. Phys. 2009, 130, 214109], and the calculation of the two electron integrals on graphics processing units (GPUs) [J. Chem. Phys. 2013, 138, 134114; J. Chem. Theory Comput. 2015, 11, 918]. To explore the parallel performance of our strong scaling implementation of the method, we present timings and extract, as its validation and first illustrative application, high-quality vibrational spectra from simulated trajectories of ß-carotene, paclitaxel, and liquid water (up to 500 atoms). We conclude that the presented BOMD scheme may be used as a cost-efficient and reliable tool for computing vibrational spectra and thermodynamics of large molecular systems including explicit solvent molecules containing 500 atoms and more. Simulating 50 ps of maitotoxin (nearly 500 atoms) employing time steps of 0.5 fs requires â¼3 weeks on 12 CPUs (Intel Xeon E5 2620 v3) with 24 GPUs (AMD FirePro 3D W8100).
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vibração
/
Simulação de Dinâmica Molecular
Idioma:
En
Revista:
J Chem Theory Comput
Ano de publicação:
2017
Tipo de documento:
Article
País de afiliação:
Alemanha
País de publicação:
Estados Unidos