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Title: A practical perspective on the implementation of hyperdynamics for accelerated simulation

Abstract

Consideration is given to several practical issues arising during the implementation of hyperdynamics, a methodology that extends the time scale of the conventional molecular dynamics simulation potentially by orders of magnitude. First, the methodology is reformulated in terms of the transition rate based on the buffer region approach (buffer rate), which can describe transitions in more general contexts than the transition state theory (TST). It will be shown that hyperdynamics can exactly preserve the buffer rate as well as the TST rate, which broadens the scope of the method. Next, the originally proposed scheme to compute the boost factor on-the-fly is reviewed and some alternative methods, one of which uses the umbrella sampling method, are presented. Finally, the methodology is validated in the context of a 1-dimensional example potential and a 3-dimensional simulation of the motion of an atomic force microscope tip moving along a surface.

Authors:
 [1]
  1. Department of Aerospace Engineering and Mechanics, The University of Minnesota, Minneapolis, Minnesota 55455 (United States)
Publication Date:
OSTI Identifier:
22255212
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 140; Journal Issue: 4; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ATOMIC FORCE MICROSCOPY; MOLECULAR DYNAMICS METHOD; ONE-DIMENSIONAL CALCULATIONS; SIMULATION; THREE-DIMENSIONAL CALCULATIONS

Citation Formats

Kim, Woo Kyun, Falk, Michael L., E-mail: mfalk@jhu.edu, Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218. A practical perspective on the implementation of hyperdynamics for accelerated simulation. United States: N. p., 2014. Web. doi:10.1063/1.4862269.
Kim, Woo Kyun, Falk, Michael L., E-mail: mfalk@jhu.edu, Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, & Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218. A practical perspective on the implementation of hyperdynamics for accelerated simulation. United States. https://doi.org/10.1063/1.4862269
Kim, Woo Kyun, Falk, Michael L., E-mail: mfalk@jhu.edu, Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218. 2014. "A practical perspective on the implementation of hyperdynamics for accelerated simulation". United States. https://doi.org/10.1063/1.4862269.
@article{osti_22255212,
title = {A practical perspective on the implementation of hyperdynamics for accelerated simulation},
author = {Kim, Woo Kyun and Falk, Michael L., E-mail: mfalk@jhu.edu and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218 and Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218},
abstractNote = {Consideration is given to several practical issues arising during the implementation of hyperdynamics, a methodology that extends the time scale of the conventional molecular dynamics simulation potentially by orders of magnitude. First, the methodology is reformulated in terms of the transition rate based on the buffer region approach (buffer rate), which can describe transitions in more general contexts than the transition state theory (TST). It will be shown that hyperdynamics can exactly preserve the buffer rate as well as the TST rate, which broadens the scope of the method. Next, the originally proposed scheme to compute the boost factor on-the-fly is reviewed and some alternative methods, one of which uses the umbrella sampling method, are presented. Finally, the methodology is validated in the context of a 1-dimensional example potential and a 3-dimensional simulation of the motion of an atomic force microscope tip moving along a surface.},
doi = {10.1063/1.4862269},
url = {https://www.osti.gov/biblio/22255212}, journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 4,
volume = 140,
place = {United States},
year = {2014},
month = {1}
}