Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

doi:10.1021/acs.jpclett.7b03254

Title: Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Journal Article · 12 March 2018 · Journal of Physical Chemistry Letters

DOI: https://doi.org/10.1021/acs.jpclett.7b03254 · OSTI ID:1470507

Sundar, Vikram ^[1]; Gelbwaser-Klimovsky, David ^[1];

^[2]

Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology
Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology; Canadian Inst. for Advanced Research, Toronto, ON (Canada)

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner–Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. Lastly, by modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Center for Excitonics (CE)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

Grant/Contract Number:: SC0001088

OSTI ID:: 1470507

Journal Information:: Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Journal Issue: 7 Vol. 9; ISSN 1948-7185

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (57)

Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis Agarwal, Pratul K.; Billeter, Salomon R.; Hammes-Schiffer, Sharon The Journal of Physical Chemistry B, Vol. 106, Issue 12 https://doi.org/10.1021/jp020190v	journal	March 2002
Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes Pérez, Alejandro; Tuckerman, Mark E. The Journal of Chemical Physics, Vol. 135, Issue 6 https://doi.org/10.1063/1.3609120	journal	August 2011
An introduction to biomolecular simulations and docking Mura, Cameron; McAnany, Charles E. Molecular Simulation, Vol. 40, Issue 10-11 https://doi.org/10.1080/08927022.2014.935372	journal	August 2014
Wigner-Kirkwood expansion: Calculation of ‘‘almost classical’’ static properties of a Lennard-Jones many-body system Barocchi, Fabrizio; Neumann, Martin; Zoppi, Marco Physical Review A, Vol. 36, Issue 5 https://doi.org/10.1103/physreva.36.2440	journal	September 1987
Asymptotic expansions and effective potentials for almost classicalN-body systems Neumann, Martin; Zoppi, Marco Physical Review A, Vol. 40, Issue 8 https://doi.org/10.1103/physreva.40.4572	journal	October 1989
Neutron diffraction of liquid neon and xenon along the coexistence line Bellissent-Funel, M. C.; Buontempo, U.; Filabozzi, A. Physical Review B, Vol. 45, Issue 9 https://doi.org/10.1103/physrevb.45.4605	journal	March 1992
Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space Habershon, Scott; Manolopoulos, David E.; Markland, Thomas E. Annual Review of Physical Chemistry, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-physchem-040412-110122	journal	April 2013
Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán Frontiers in Chemistry, Vol. 1 https://doi.org/10.3389/fchem.2013.00026	journal	January 2013
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
Polarizable force field development for lipids and their efficient applications in membrane proteins Chu, Huiying; Cao, Liaoran; Peng, Xiangda WIREs Computational Molecular Science, Vol. 7, Issue 5 https://doi.org/10.1002/wcms.1312	journal	April 2017
Many-body and quantum effects in the radial distribution function of liquid neon and argon Ermakova, Elena; Solca, Jan; Huber, Hanspeter Chemical Physics Letters, Vol. 246, Issue 3 https://doi.org/10.1016/0009-2614(95)01108-L	journal	November 1995
The equation of state of neon between 27 and 70 K Gibbons, R. M. Cryogenics, Vol. 9, Issue 4 https://doi.org/10.1016/0011-2275(69)90231-8	journal	August 1969
Theory and application of the quantum phase-space distribution functions Lee, Hai-Woong Physics Reports, Vol. 259, Issue 3 https://doi.org/10.1016/0370-1573(95)00007-4	journal	August 1995
Force Fields for Protein Simulations Ponder, Jay W.; Case, David A. Protein Simulations https://doi.org/10.1016/S0065-3233(03)66002-X	book	January 2003
Centroid molecular dynamics: A quantum dynamics method suitable for the parallel computer Pavese, Marc; Jang, Soonmin; Voth, Gregory A. Parallel Computing, Vol. 26, Issue 7-8 https://doi.org/10.1016/S0167-8191(00)00025-9	journal	July 2000
Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges Ceriotti, Michele; Fang, Wei; Kusalik, Peter G. Chemical Reviews, Vol. 116, Issue 13 https://doi.org/10.1021/acs.chemrev.5b00674	journal	April 2016
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation Eastman, Peter; Friedrichs, Mark S.; Chodera, John D. Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct300857j	journal	November 2012
Nuclear Quantum Effects and Hydrogen Bonding in Liquids Raugei, Simone; Klein, Michael L. Journal of the American Chemical Society, Vol. 125, Issue 30 https://doi.org/10.1021/ja0351995	journal	July 2003
The Semiclassical Initial Value Representation: A Potentially Practical Way for Adding Quantum Effects to Classical Molecular Dynamics Simulations Miller, William H. The Journal of Physical Chemistry A, Vol. 105, Issue 13 https://doi.org/10.1021/jp003712k	journal	April 2001
Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis Agarwal, Pratul K.; Billeter, Salomon R.; Hammes-Schiffer, Sharon The Journal of Physical Chemistry B, Vol. 106, Issue 12 https://doi.org/10.1021/jp020190v	journal	March 2002
Wigner function approach to the quantum Brownian motion of a particle in a potential Coffey, W. T.; Kalmykov, Yu. P.; Titov, S. V. Physical Chemistry Chemical Physics, Vol. 9, Issue 26 https://doi.org/10.1039/b614554j	journal	January 2007
Force fields and molecular dynamics simulations González, M. A. École thématique de la Société Française de la Neutronique, Vol. 12 https://doi.org/10.1051/sfn/201112009	journal	January 2011
Applications of higher order composite factorization schemes in imaginary time path integral simulations Jang, Seogjoo; Jang, Soonmin; Voth, Gregory A. The Journal of Chemical Physics, Vol. 115, Issue 17 https://doi.org/10.1063/1.1410117	journal	November 2001
Forward–backward semiclassical dynamics for quantum fluids using pair propagators: Application to liquid para -hydrogen Nakayama, Akira; Makri, Nancy The Journal of Chemical Physics, Vol. 119, Issue 16 https://doi.org/10.1063/1.1611473	journal	October 2003
Practical evaluation of condensed phase quantum correlation functions: A Feynman–Kleinert variational linearized path integral method Poulsen, Jens Aage; Nyman, Gunnar; Rossky, Peter J. The Journal of Chemical Physics, Vol. 119, Issue 23 https://doi.org/10.1063/1.1626631	journal	December 2003
Structure Study of Liquid Neon by Neutron Diffraction de Graaf, L. A.; Mozer, B. The Journal of Chemical Physics, Vol. 55, Issue 10 https://doi.org/10.1063/1.1675607	journal	November 1971
Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: Proton transfer in triosephosphate isomerase Wang, Mingliang; Lu, Zhenyu; Yang, Weitao The Journal of Chemical Physics, Vol. 124, Issue 12 https://doi.org/10.1063/1.2181145	journal	March 2006
An accurate and simple quantum model for liquid water Paesani, Francesco; Zhang, Wei; Case, David A. The Journal of Chemical Physics, Vol. 125, Issue 18 https://doi.org/10.1063/1.2386157	journal	November 2006
An efficient ring polymer contraction scheme for imaginary time path integral simulations Markland, Thomas E.; Manolopoulos, David E. The Journal of Chemical Physics, Vol. 129, Issue 2 https://doi.org/10.1063/1.2953308	journal	July 2008
A fast path integral method for polarizable force fields Fanourgakis, George S.; Markland, Thomas E.; Manolopoulos, David E. The Journal of Chemical Physics, Vol. 131, Issue 9 https://doi.org/10.1063/1.3216520	journal	January 2009
Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum Liu, Jian; Miller, William H.; Paesani, Francesco The Journal of Chemical Physics, Vol. 131, Issue 16 https://doi.org/10.1063/1.3254372	journal	October 2009
Accelerating the convergence of path integral dynamics with a generalized Langevin equation Ceriotti, Michele; Manolopoulos, David E.; Parrinello, Michele The Journal of Chemical Physics, Vol. 134, Issue 8 https://doi.org/10.1063/1.3556661	journal	February 2011
Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes Pérez, Alejandro; Tuckerman, Mark E. The Journal of Chemical Physics, Vol. 135, Issue 6 https://doi.org/10.1063/1.3609120	journal	August 2011
Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids Chandler, David; Wolynes, Peter G. The Journal of Chemical Physics, Vol. 74, Issue 7 https://doi.org/10.1063/1.441588	journal	April 1981
Molecular dynamics study of the structural and thermodynamic properties of MgO crystal with quantum correction Matsui, Masanori The Journal of Chemical Physics, Vol. 91, Issue 1 https://doi.org/10.1063/1.457484	journal	July 1989
Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A. The Journal of Chemical Physics, Vol. 143, Issue 11 https://doi.org/10.1063/1.4930848	journal	September 2015
*Ab initio*potential energy curve for the neon atom pair and thermophysical properties of the dilute neon gas. I. Neon–neon interatomic potential and rovibrational spectra Hellmann, Robert; Bich, Eckard; Vogel, Eckhard Molecular Physics, Vol. 106, Issue 1 https://doi.org/10.1080/00268970701843147	journal	January 2008
Nuclear quantum effects in liquid water from path-integral simulations using an ab initio force-matching approach Spura, Thomas; John, Christopher; Habershon, Scott Molecular Physics, Vol. 113, Issue 8 https://doi.org/10.1080/00268976.2014.981231	journal	November 2014
Liquid argon: Monte carlo and molecular dynamics calculations Barker, J. A.; Fisher, R. A.; Watts, R. O. Molecular Physics, Vol. 21, Issue 4 https://doi.org/10.1080/00268977100101821	journal	January 1971
Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble Panagiotopoulos, Athanassios Z. Molecular Physics, Vol. 61, Issue 4 https://doi.org/10.1080/00268978700101491	journal	July 1987
Phase equilibria by simulation in the Gibbs ensemble: Alternative derivation, generalization and application to mixture and membrane equilibria Panagiotopoulos, A. Z.; Quirke, N.; Stapleton, M. Molecular Physics, Vol. 63, Issue 4 https://doi.org/10.1080/00268978800100361	journal	March 1988
MCCCS Towhee: a tool for Monte Carlo molecular simulation Martin, Marcus G. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.828208	journal	December 2013
Influence of simulation protocols on the efficiency of Gibbs ensemble Monte Carlo simulations Cortés Morales, Angel D.; Economou, Ioannis G.; Peters, Cornelis J. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.828209	journal	December 2013
An introduction to biomolecular simulations and docking Mura, Cameron; McAnany, Charles E. Molecular Simulation, Vol. 40, Issue 10-11 https://doi.org/10.1080/08927022.2014.935372	journal	August 2014
Path-Integral Calculation of the Two-Particle Slater Sum for He 4 Fosdick, Lloyd D.; Jordan, Harry F. Physical Review, Vol. 143, Issue 1 https://doi.org/10.1103/PhysRev.143.58	journal	March 1966
On the Quantum Correction For Thermodynamic Equilibrium Wigner, E. Physical Review, Vol. 40, Issue 5 https://doi.org/10.1103/PhysRev.40.749	journal	June 1932
Quantum Statistics of Almost Classical Assemblies Kirkwood, John G. Physical Review, Vol. 44, Issue 1 https://doi.org/10.1103/PhysRev.44.31	journal	July 1933
Molecular-dynamics calculation of the quantum corrections to the pair-distribution function for a Lennard-Jones fluid Barocchi, F.; Neumann, M.; Zoppi, M. Physical Review A, Vol. 29, Issue 3 https://doi.org/10.1103/PhysRevA.29.1331	journal	March 1984
Time dependence of a general class of quantum distribution functions O'Connell, R. F.; Wang, Lipo; Williams, H. A. Physical Review A, Vol. 30, Issue 5 https://doi.org/10.1103/PhysRevA.30.2187	journal	November 1984
Quantum-corrected pair distribution function of liquid neon Barocchi, F.; Neumann, M.; Zoppi, M. Physical Review A, Vol. 31, Issue 6 https://doi.org/10.1103/PhysRevA.31.4015	journal	June 1985
Wigner-Kirkwood expansion: Calculation of ‘‘almost classical’’ static properties of a Lennard-Jones many-body system Barocchi, Fabrizio; Neumann, Martin; Zoppi, Marco Physical Review A, Vol. 36, Issue 5 https://doi.org/10.1103/PhysRevA.36.2440	journal	September 1987
Asymptotic expansions and effective potentials for almost classicalN-body systems Neumann, Martin; Zoppi, Marco Physical Review A, Vol. 40, Issue 8 https://doi.org/10.1103/PhysRevA.40.4572	journal	October 1989
Neutron diffraction of liquid neon and xenon along the coexistence line Bellissent-Funel, M. C.; Buontempo, U.; Filabozzi, A. Physical Review B, Vol. 45, Issue 9 https://doi.org/10.1103/PhysRevB.45.4605	journal	March 1992
Biomolecular Simulation: A Computational Microscope for Molecular Biology Dror, Ron O.; Dirks, Robert M.; Grossman, J. P. Annual Review of Biophysics, Vol. 41, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155245	journal	June 2012
Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space Habershon, Scott; Manolopoulos, David E.; Markland, Thomas E. Annual Review of Physical Chemistry, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-physchem-040412-110122	journal	April 2013
Amber 2017, University of California, San Francisco Case, D. A.; Cerutti, D. S.; Cheatham, T. E. University of California, San Francisco https://doi.org/10.13140/rg.2.2.36172.41606	dataset	January 2017
Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán Frontiers in Chemistry, Vol. 1 https://doi.org/10.3389/fchem.2013.00026	journal	January 2013

Similar Records

Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics

Journal Article · 2015 · Journal of Chemical Physics · OSTI ID:22415782

Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea

NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field (ALCF-2 Early Science Program Technical Report)

Technical Report · 2013 · OSTI ID:1079771

Roux, Benoit; Luo, Yun (Lyna); Jiang, Wei

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

Journal Article · 2017 · Journal of Chemical Physics · OSTI ID:1498059

Tao, Xuecheng; Shushkov, Philip; Miller, III, Thomas F.

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
charge transport
optics
photosynthesis (natural and artificial)
solar (photovoltaic)
solid state lighting
synthesis (novel materials)
synthesis (scalable processing)
synthesis (self-assembly)

Title: Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Citation Formats

References (57)

Similar Records

Related Subjects