The Adaptive Buffered Force QM/MM Method in the CP2K and AMBER Software Packages

Letif Mones*, Andrew Jones, Andreas W. Goetz, Teodoro Laino, Ross C. Walker, Ben Leimkuhler, Gabor Csanyi, Noam Bernstein

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. 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. (c) 2015 Wiley Periodicals, Inc.

Original languageEnglish
Pages (from-to)633-648
Number of pages16
JournalJournal of Computational Chemistry
Volume36
Issue number9
DOIs
Publication statusPublished - 5 Apr 2015

Keywords

  • quantum-mechanics
  • molecular-mechanics
  • adaptive quantum-mechanics
  • force-mixing
  • multiscale
  • MOLECULAR-DYNAMICS SIMULATION
  • SEMIEMPIRICAL METHODS
  • MULTISCALE SIMULATIONS
  • ENZYMATIC-REACTIONS
  • CHEMICAL-REACTIONS
  • SYSTEMS
  • DENSITY
  • PARAMETERS
  • APPROXIMATIONS
  • MODEL

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