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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];  [1];  [7]
+ Show Author Affiliations
  1. Engineering Department University of Cambridge Cambridge CB2 1PZ United Kingdom
  2. Institute for Condensed Matter and Complex Systems School of Physics and Astronomy University of Edinburgh Edinburgh EH9 3JZ United Kingdom
  3. San Diego Supercomputer Center University of California San Diego La Jolla California 92093
  4. Mathematical and Computational Sciences Department IBM Research–Zurich Säumerstrasse 4 8803 Rüschlikon Switzerland
  5. San Diego Supercomputer Center University of California San Diego La Jolla California 92093, Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093
  6. The Maxwell Institute and School of Mathematics, University of Edinburgh Edinburgh EH9 3JZ United Kingdom
  7. Center for Computational Material Science Naval Research Laboratory Washington DC 20375
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:  
DE‐AC36‐99GO‐10337; AC36-99GO10337; OCI-1148358; ACI-1053575; EP/G036136/1; EP/J01298X/1; GM100934
Resource Type:
Published Article
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Name: Journal of Computational Chemistry Journal Volume: 36 Journal Issue: 9; Journal ID: ISSN 0192-8651
Publisher:
Wiley Blackwell (John Wiley & Sons)
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.
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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. https://doi.org/10.1002/jcc.23839
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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. https://doi.org/10.1002/jcc.23839.
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@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 = {Tue Feb 03 00:00:00 EST 2015},
month = {Tue Feb 03 00:00:00 EST 2015}
}
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Works referenced in this record:

Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
journal, November 2010

  • Korth, Martin
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 12
  • DOI: 10.1021/ct100408b

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling
journal, November 2005

  • Laino, Teodoro; Mohamed, Fawzi; Laio, Alessandro
  • Journal of Chemical Theory and Computation, Vol. 1, Issue 6
  • DOI: 10.1021/ct050123f

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations
journal, August 2006

  • Laino, Teodoro; Mohamed, Fawzi; Laio, Alessandro
  • Journal of Chemical Theory and Computation, Vol. 2, Issue 5
  • DOI: 10.1021/ct6001169

Density-functional exchange-energy approximation with correct asymptotic behavior
journal, September 1988

Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
journal, January 1996

  • Bakowies, Dirk; Thiel, Walter
  • The Journal of Physical Chemistry, Vol. 100, Issue 25
  • DOI: 10.1021/jp9536514

Results obtained with the correlation energy density functionals of becke and Lee, Yang and Parr
journal, May 1989

Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
journal, October 1993

  • Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
  • Journal of the American Chemical Society, Vol. 115, Issue 21
  • DOI: 10.1021/ja00074a030

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005

  • Praprotnik, Matej; Delle Site, Luigi; Kremer, Kurt
  • The Journal of Chemical Physics, Vol. 123, Issue 22
  • DOI: 10.1063/1.2132286

Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes
journal, December 2005

  • Rode, Bernd M.; Hofer, Thomas S.; Randolf, Bernhard R.
  • Theoretical Chemistry Accounts, Vol. 115, Issue 2-3
  • DOI: 10.1007/s00214-005-0049-1

Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids
journal, June 2006

Density, structure, and dynamics of water: The effect of van der Waals interactions
journal, January 2011

  • Wang, Jue; Román-Pérez, G.; Soler, Jose M.
  • The Journal of Chemical Physics, Vol. 134, Issue 2
  • DOI: 10.1063/1.3521268

ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase
journal, April 2002

QM/MM Methods for Biomolecular Systems
journal, January 2009

  • Senn, Hans Martin; Thiel, Walter
  • Angewandte Chemie International Edition, Vol. 48, Issue 7
  • DOI: 10.1002/anie.200802019

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Why nature really chose phosphate
journal, January 2013

  • Kamerlin, Shina C. L.; Sharma, Pankaz K.; Prasad, Ram B.
  • Quarterly Reviews of Biophysics, Vol. 46, Issue 1
  • DOI: 10.1017/S0033583512000157

Coordination numbers as reaction coordinates in constrained molecular dynamics
journal, January 1998

Comparison of multiple Amber force fields and development of improved protein backbone parameters
journal, November 2006

  • Hornak, Viktor; Abel, Robert; Okur, Asim
  • Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3
  • DOI: 10.1002/prot.21123

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms
journal, January 2007

  • Nam, Kwangho; Cui, Qiang; Gao, Jiali
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 2
  • DOI: 10.1021/ct6002466

Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results
journal, January 1992

  • Thiel, Walter; Voityuk, Alexander A.
  • Theoretica Chimica Acta, Vol. 81, Issue 6
  • DOI: 10.1007/BF01134863

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
journal, June 1985

  • Dewar, Michael J. S.; Zoebisch, Eve G.; Healy, Eamonn F.
  • Journal of the American Chemical Society, Vol. 107, Issue 13
  • DOI: 10.1021/ja00299a024

Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
journal, August 1993

  • Tuckerman, Mark E.; Berne, Bruce J.; Martyna, Glenn J.
  • The Journal of Chemical Physics, Vol. 99, Issue 4
  • DOI: 10.1063/1.465188

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method
journal, August 2008

  • Akin-Ojo, Omololu; Song, Yang; Wang, Feng
  • The Journal of Chemical Physics, Vol. 129, Issue 6
  • DOI: 10.1063/1.2965882

Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: “Umbrella integration”
journal, October 2005

  • Kästner, Johannes; Thiel, Walter
  • The Journal of Chemical Physics, Vol. 123, Issue 14
  • DOI: 10.1063/1.2052648

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
journal, October 1993

  • Bayly, Christopher I.; Cieplak, Piotr; Cornell, Wendy
  • The Journal of Physical Chemistry, Vol. 97, Issue 40
  • DOI: 10.1021/j100142a004

Dynamic QM/MM: A Hybrid Approach to Simulating Gas-Liquid Interactions
book, January 2011

  • Yockel, Scott; Schatz, George C.
  • Multiscale Molecular Methods in Applied Chemistry
  • DOI: 10.1007/128_2011_130

Multiscale Modeling of Chemistry in Water: Are We There Yet?
journal, November 2013

  • Bulo, Rosa E.; Michel, Carine; Fleurat-Lessard, Paul
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 12
  • DOI: 10.1021/ct4005596

A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
journal, June 1998

  • Gao, Jiali; Amara, Patricia; Alhambra, Cristobal
  • The Journal of Physical Chemistry A, Vol. 102, Issue 24
  • DOI: 10.1021/jp9809890

RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I
journal, July 2006

  • Rocha, Gerd B.; Freire, Ricardo O.; Simas, Alfredo M.
  • Journal of Computational Chemistry, Vol. 27, Issue 10
  • DOI: 10.1002/jcc.20425

Energetics and Dynamics of Enzymatic Reactions
journal, August 2001

  • Villà, Jordi; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 105, Issue 33
  • DOI: 10.1021/jp011048h

The Solvation Structure of Na + and K + in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations
journal, March 2012

  • Rowley, Christopher N.; Roux, Benoı̂t
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 10
  • DOI: 10.1021/ct300091w

The quest for the best nonpolarizable water model from the adaptive force matching method
journal, August 2010

  • Akin-Ojo, Omololu; Wang, Feng
  • Journal of Computational Chemistry, Vol. 32, Issue 3
  • DOI: 10.1002/jcc.21634

A pseudobond approach to combining quantum mechanical and molecular mechanical methods
journal, January 1999

  • Zhang, Yingkai; Lee, Tai-Sung; Yang, Weitao
  • The Journal of Chemical Physics, Vol. 110, Issue 1
  • DOI: 10.1063/1.478083

An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package
journal, September 2012

  • Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2
  • DOI: 10.1002/wcms.1121

Optimization of parameters for semiempirical methods I. Method
journal, March 1989

On the Convergence of QM/MM Energies
journal, February 2011

  • Hu, LiHong; Söderhjelm, Pär; Ryde, Ulf
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 3
  • DOI: 10.1021/ct100530r

A QM/MM simulation method applied to the solution of Li+ in liquid ammonia
journal, November 1996

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988

Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems
journal, July 2012

  • Park, Kyoyeon; Götz, Andreas W.; Walker, Ross C.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 8
  • DOI: 10.1021/ct300331f

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

  • Darden, Tom; York, Darrin; Pedersen, Lee
  • The Journal of Chemical Physics, Vol. 98, Issue 12
  • DOI: 10.1063/1.464397

Toward a Practical Method for Adaptive QM/MM Simulations
journal, July 2009

  • Bulo, Rosa E.; Ensing, Bernd; Sikkema, Jetze
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct900148e

A Gentle Stochastic Thermostat for Molecular Dynamics
journal, April 2009

  • Leimkuhler, Ben; Noorizadeh, Emad; Theil, Florian
  • Journal of Statistical Physics, Vol. 135, Issue 2
  • DOI: 10.1007/s10955-009-9734-0

Force field design for metalloproteins
journal, October 1991

  • Hoops, Stephen C.; Anderson, Kenneth W.; Merz, Kenneth M.
  • Journal of the American Chemical Society, Vol. 113, Issue 22
  • DOI: 10.1021/ja00022a010

Hybrid atomistic simulation methods for materials systems
journal, January 2009

Basic ideas for the correction of semiempirical methods describing H-bonded systems
journal, November 2000

Adaptive stochastic methods for sampling driven molecular systems
journal, August 2011

  • Jones, Andrew; Leimkuhler, Ben
  • The Journal of Chemical Physics, Vol. 135, Issue 8
  • DOI: 10.1063/1.3626941

Separable dual-space Gaussian pseudopotentials
journal, July 1996

Semiempirical Self-Consistent Polarization Description of Bulk Water, the Liquid−Vapor Interface, and Cubic Ice
journal, June 2011

  • Murdachaew, Garold; Mundy, Christopher J.; Schenter, Gregory K.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 23
  • DOI: 10.1021/jp110481m

Topologically Invariant Reaction Coordinates for Simulating Multistate Chemical Reactions
journal, December 2012

  • Mones, Letif; Csányi, Gábor
  • The Journal of Physical Chemistry B, Vol. 116, Issue 51
  • DOI: 10.1021/jp307648s

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics
journal, March 2007

  • Ensing, Bernd; Nielsen, Steven O.; Moore, Preston B.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 3
  • DOI: 10.1021/ct600323n

QM/MM simulation of liquid water with an adaptive quantum region
journal, January 2012

  • Bernstein, Noam; Várnai, Csilla; Solt, Iván
  • Phys. Chem. Chem. Phys., Vol. 14, Issue 2
  • DOI: 10.1039/C1CP22600B

The implementation of a fast and accurate QM/MM potential method in Amber
journal, January 2008

  • Walker, Ross C.; Crowley, Michael F.; Case, David A.
  • Journal of Computational Chemistry, Vol. 29, Issue 7
  • DOI: 10.1002/jcc.20857

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
journal, September 2007

Semiempirical GGA-type density functional constructed with a long-range dispersion correction
journal, January 2006

  • Grimme, Stefan
  • Journal of Computational Chemistry, Vol. 27, Issue 15, p. 1787-1799
  • DOI: 10.1002/jcc.20495

Ground states of molecules. 38. The MNDO method. Approximations and parameters
journal, June 1977

  • Dewar, Michael J. S.; Thiel, Walter
  • Journal of the American Chemical Society, Vol. 99, Issue 15
  • DOI: 10.1021/ja00457a004

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations
journal, October 2004

  • Nam, Kwangho; Gao, Jiali; York, Darrin M.
  • Journal of Chemical Theory and Computation, Vol. 1, Issue 1
  • DOI: 10.1021/ct049941i

“Learn on the Fly”: A Hybrid Classical and Quantum-Mechanical Molecular Dynamics Simulation
journal, October 2004

An extensible interface for QM/MM molecular dynamics simulations with AMBER
journal, October 2013

  • Götz, Andreas W.; Clark, Matthew A.; Walker, Ross C.
  • Journal of Computational Chemistry, Vol. 35, Issue 2
  • DOI: 10.1002/jcc.23444

Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations
journal, March 2007

  • Heyden, Andreas; Lin, Hai; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 9
  • DOI: 10.1021/jp0673617

Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water
journal, August 2011

  • Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 32
  • DOI: 10.1021/jp203436e

Notes on “Ewald summation of electrostatic multipole interactions up to quadrupolar level” [J. Chem. Phys. 119, 7471 (2003)]
journal, August 2008

  • Laino, Teodoro; Hutter, Jürg
  • The Journal of Chemical Physics, Vol. 129, Issue 7
  • DOI: 10.1063/1.2970887

Die Berechnung optischer und elektrostatischer Gitterpotentiale
journal, January 1921

Evaluating Boundary Dependent Errors in QM/MM Simulations
journal, April 2009

  • Solt, Iván; Kulhánek, Petr; Simon, István
  • The Journal of Physical Chemistry B, Vol. 113, Issue 17
  • DOI: 10.1021/jp807277r

Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations
journal, January 2008

  • Heyden, Andreas; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 2
  • DOI: 10.1021/ct700269m

Tests of an Adaptive QM/MM Calculation on Free Energy Profiles of Chemical Reactions in Solution
journal, September 2013

  • Várnai, Csilla; Bernstein, Noam; Mones, Letif
  • The Journal of Physical Chemistry B, Vol. 117, Issue 40
  • DOI: 10.1021/jp405974b

Thermostats for “Slow” Configurational Modes
journal, July 2007

  • Samoletov, Alex A.; Dettmann, Carl P.; Chaplain, Mark A. J.
  • Journal of Statistical Physics, Vol. 128, Issue 6
  • DOI: 10.1007/s10955-007-9365-2
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