Abstract
A method of molecular dynamics with quantum corrections, practical for studies of large molecular systems, is reviewed. The approach is based on the Bohmian formulation of the time-dependent Schrödinger equation in which a wavefunction is represented by an ensemble of interdependent trajectories. The quantum effects come from the quantum potential acting on trajectories on par with the usual classical potential. The quantum potential is determined from the evolving nuclear wavefunction, i.e. from the quantum trajectory (QT) ensemble itself. For practical and conceptual reasons the quantum potential and corresponding quantum nuclear effect are computed only for the selected light nuclei. For studies of reactive chemical processes, the classical potential is computed on-the-fly using the density functional tight binding method of electronic structure. A massively parallel implementation, based on the message passing interface allows for efficient simulations of ensembles of thousands of trajectories describing systems of up to 200 atoms. As a biochemical application, the approximate QT approach is used to model the tunnelling-dominated proton transfer in soybean-lipoxygenase-1. A materials science application is represented by a study of the nuclear quantum effect on adsorption of hydrogen and deuterium on a C37H15 molecule, which is a model flake of graphene.
Original language | English |
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Pages (from-to) | 86-106 |
Number of pages | 21 |
Journal | Molecular Simulation |
Volume | 41 |
Issue number | 1-3 |
DOIs | |
State | Published - Feb 11 2015 |
Externally published | Yes |
Funding
Acknowledgment is made to the donors of the American Chemical Society Petroleum Research Fund for partial support of this research (S.G.) and to SC EPSCoR:GEAR-CI program (V. R.). This material is based upon work partially supported by the National Science Foundation under Grants No. CHE-1056188 (S. G.) and ARRA-NSF-EPS-0919436 (J.J.). XSEDE allocation TG-DMR110037 time on Kraken at the National Institute for Computational Sciences and use of USC HPC cluster funded by the National Science Foundation under Grant No. CHE-1048629 are also acknowledged.
Keywords
- densityfunctional tight-binding method
- hybrid dynamics of quantum/classical nuclei
- on-the-fly electronic structure
- quantum effect