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Title: The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

Abstract

We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8]
  1. Univ. of Cambridge (United Kingdom). Engineering Dept.
  2. Univ. of Edinburgh, Scotland (United Kingdom). Inst. for Condensed Matter and Complex Systems, School of Physics and Astronomy
  3. Univ. of California, San Diego, CA (United States). San Diego Supercomputer Center
  4. IBM Research-Zurich (Switzerland). Mathematical and Computational Sciences Dept.
  5. Univ. of California, San Diego, CA (United States). San Diego Supercomputer Center; Univ. of California, San Diego, CA (United States). Dept. of Chemistry and Biochemistry
  6. Univ. of Edinburgh, Scotland (United Kingdom). The Maxwell Inst. and School of Mathematics
  7. Univ. of Cambridge (United Kingdom). Engineering Dept
  8. Naval Research Lab. (NRL), Washington, DC (United States). Center for Computational Material Science
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1345677
Alternate Identifier(s):
OSTI ID: 1343098; OSTI ID: 1345678
Grant/Contract Number:  
AC36-99GO10337; OCI-1148358; ACI-1053575; EP/G036136/1; EP/J01298X/1; GM100934; AC36-99GO-10337
Resource Type:
Published Article
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Volume: 36; Journal Issue: 9; Journal ID: ISSN 0192-8651
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; quantum-mechanics/molecular-mechanics; adaptive quantum-mechanics/molecular-mechanics; force-mixing; multiscale

Citation Formats

Mones, Letif, Jones, Andrew, Götz, Andreas W., Laino, Teodoro, Walker, Ross C., Leimkuhler, Ben, Csányi, Gábor, and Bernstein, Noam. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. United States: N. p., 2015. Web. doi:10.1002/jcc.23839.
Mones, Letif, Jones, Andrew, Götz, Andreas W., Laino, Teodoro, Walker, Ross C., Leimkuhler, Ben, Csányi, Gábor, & Bernstein, Noam. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. United States. doi:10.1002/jcc.23839.
Mones, Letif, Jones, Andrew, Götz, Andreas W., Laino, Teodoro, Walker, Ross C., Leimkuhler, Ben, Csányi, Gábor, and Bernstein, Noam. Tue . "The adaptive buffered force QM/MM method in the CP2K and AMBER software packages". United States. doi:10.1002/jcc.23839.
@article{osti_1345677,
title = {The adaptive buffered force QM/MM method in the CP2K and AMBER software packages},
author = {Mones, Letif and Jones, Andrew and Götz, Andreas W. and Laino, Teodoro and Walker, Ross C. and Leimkuhler, Ben and Csányi, Gábor and Bernstein, Noam},
abstractNote = {We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.},
doi = {10.1002/jcc.23839},
journal = {Journal of Computational Chemistry},
number = 9,
volume = 36,
place = {United States},
year = {2015},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/jcc.23839

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Cited by: 13 works
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