Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

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

Journal Article · · Journal of Computational Chemistry
DOI:https://doi.org/10.1002/jcc.23839· OSTI ID:1345677
 [1];  [2];  [3];  [4];  [5];  [6];  [1];  [7]
  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
+ Show Author Affiliations

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. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Research Organization:
Univ. of California, San Diego, CA (United States)
Sponsoring Organization:
National Inst. of Health (NIH); National Science Foundation (NSF); USDOE
Grant/Contract Number:
AC36-99GO10337
OSTI ID:
1345677
Alternate ID(s):
OSTI ID: 1343098
OSTI ID: 1345678
Journal Information:
Journal of Computational Chemistry, Journal Name: Journal of Computational Chemistry Journal Issue: 9 Vol. 36; ISSN 0192-8651
Publisher:
Wiley Blackwell (John Wiley & Sons)Copyright Statement
Country of Publication:
United States
Language:
English

References (70)

Die Berechnung optischer und elektrostatischer Gitterpotentiale journal January 1921
QM/MM Methods for Biomolecular Systems journal January 2009
RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I journal July 2006
Semiempirical GGA-type density functional constructed with a long-range dispersion correction journal January 2006
The implementation of a fast and accurate QM/MM potential method in Amber journal January 2008
The quest for the best nonpolarizable water model from the adaptive force matching method journal August 2010
An extensible interface for QM/MM molecular dynamics simulations with AMBER journal October 2013
A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers journal December 1986
Optimization of parameters for semiempirical methods I. Method journal March 1989
Comparison of multiple Amber force fields and development of improved protein backbone parameters journal November 2006
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package
  • Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2 https://doi.org/10.1002/wcms.1121
journal September 2012
Dynamic QM/MM: A Hybrid Approach to Simulating Gas-Liquid Interactions book January 2011
Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results journal January 1992
Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes journal December 2005
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements journal September 2007
Thermostats for “Slow” Configurational Modes journal July 2007
A Gentle Stochastic Thermostat for Molecular Dynamics journal April 2009
Results obtained with the correlation energy density functionals of becke and Lee, Yang and Parr journal May 1989
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme journal May 1976
A QM/MM simulation method applied to the solution of Li+ in liquid ammonia journal November 1996
Basic ideas for the correction of semiempirical methods describing H-bonded systems journal November 2000
ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase journal April 2002
Why nature really chose phosphate journal January 2013
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations journal October 2004
An Efficient Real Space Multigrid QM/MM Electrostatic Coupling journal November 2005
Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields journal November 2010
On the Convergence of QM/MM Energies journal February 2011
The Solvation Structure of Na + and K + in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations journal March 2012
Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems journal July 2012
Multiscale Modeling of Chemistry in Water: Are We There Yet? journal November 2013
An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations journal August 2006
Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms journal January 2007
Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics journal March 2007
Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations journal January 2008
Toward a Practical Method for Adaptive QM/MM Simulations journal July 2009
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model journal October 1993
Force field design for metalloproteins journal October 1991
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation journal October 1993
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model journal June 1985
Ground states of molecules. 38. The MNDO method. Approximations and parameters journal June 1977
Energetics and Dynamics of Enzymatic Reactions journal August 2001
Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations journal March 2007
Semiempirical Self-Consistent Polarization Description of Bulk Water, the Liquid−Vapor Interface, and Cubic Ice journal June 2011
Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water journal August 2011
Topologically Invariant Reaction Coordinates for Simulating Multistate Chemical Reactions journal December 2012
Tests of an Adaptive QM/MM Calculation on Free Energy Profiles of Chemical Reactions in Solution journal September 2013
Evaluating Boundary Dependent Errors in QM/MM Simulations journal April 2009
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches journal January 1996
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal April 1998
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations journal June 1998
QM/MM simulation of liquid water with an adaptive quantum region journal January 2012
Coordination numbers as reaction coordinates in constrained molecular dynamics journal January 1998
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: “Umbrella integration” journal October 2005
Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly journal December 2005
Canonical sampling through velocity rescaling journal January 2007
Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method journal August 2008
Notes on “Ewald summation of electrostatic multipole interactions up to quadrupolar level” [J. Chem. Phys. 119, 7471 (2003)] journal August 2008
Density, structure, and dynamics of water: The effect of van der Waals interactions journal January 2011
Adaptive stochastic methods for sampling driven molecular systems journal August 2011
Generalized Langevin equation approach for atom/solid-surface scattering: General formulation for classical scattering off harmonic solids journal January 1976
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals journal August 1993
A pseudobond approach to combining quantum mechanical and molecular mechanical methods journal January 1999
Hybrid atomistic simulation methods for materials systems journal January 2009
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon journal May 1995
Separable dual-space Gaussian pseudopotentials journal July 1996
Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids journal June 2006
“Learn on the Fly”: A Hybrid Classical and Quantum-Mechanical Molecular Dynamics Simulation journal October 2004

Similar Records

Accuracy of buffered-force QM/MM simulations of silica
Journal Article · Fri Feb 13 23:00:00 EST 2015 · Journal of Chemical Physics · OSTI ID:22416100

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
97 MATHEMATICS AND COMPUTING
adaptive quantum-mechanics/molecular-mechanics
force-mixing
multiscale
quantum-mechanics/molecular-mechanics