1
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Althorpe SC. Path Integral Simulations of Condensed-Phase Vibrational Spectroscopy. Annu Rev Phys Chem 2024; 75:397-420. [PMID: 38941531 DOI: 10.1146/annurev-physchem-090722-124705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Recent theoretical and algorithmic developments have improved the accuracy with which path integral dynamics methods can include nuclear quantum effects in simulations of condensed-phase vibrational spectra. Such methods are now understood to be approximations to the delocalized classical Matsubara dynamics of smooth Feynman paths, which dominate the dynamics of systems such as liquid water at room temperature. Focusing mainly on simulations of liquid water and hexagonal ice, we explain how the recently developed quasicentroid molecular dynamics (QCMD), fast-QCMD, and temperature-elevated path integral coarse-graining simulations (Te PIGS) methods generate classical dynamics on potentials of mean force obtained by averaging over quantum thermal fluctuations. These new methods give very close agreement with one another, and the Te PIGS method has recently yielded excellent agreement with experimentally measured vibrational spectra for liquid water, ice, and the liquid-air interface. We also discuss the limitations of such methods.
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Affiliation(s)
- Stuart C Althorpe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom;
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2
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Atsango AO, Morawietz T, Marsalek O, Markland TE. Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations. J Chem Phys 2023; 159:074101. [PMID: 37581418 DOI: 10.1063/5.0162066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics simulations to model the bond breaking and formation involved in proton transfer and path-integral simulations to model the nuclear quantum effects relevant to light hydrogen atoms. These requirements result in a prohibitive computational cost, especially at the time and length scales needed to converge proton transport properties. Here, we present machine-learned potentials (MLPs) that can model both excess protons and hydroxide ions at the generalized gradient approximation and hybrid density functional theory levels of accuracy and use them to perform multiple nanoseconds of both classical and path-integral proton defect simulations at a fraction of the cost of the corresponding ab initio simulations. We show that the MLPs are able to reproduce ab initio trends and converge properties such as the diffusion coefficients of both excess protons and hydroxide ions. We use our multi-nanosecond simulations, which allow us to monitor large numbers of proton transfer events, to analyze the role of hypercoordination in the transport mechanism of the hydroxide ion and provide further evidence for the asymmetry in diffusion between excess protons and hydroxide ions.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ondrej Marsalek
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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3
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Plé T, Mauger N, Adjoua O, Inizan TJ, Lagardère L, Huppert S, Piquemal JP. Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: From Force Fields to Machine Learning Potentials. J Chem Theory Comput 2023; 19:1432-1445. [PMID: 36856658 DOI: 10.1021/acs.jctc.2c01233] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP, exploits two simulation strategies: the Ring-Polymer Molecular Dynamics (RPMD) that provides exact structural properties at the cost of a MD simulation in an extended space of multiple replicas and the adaptive Quantum Thermal Bath (adQTB) that imposes the quantum distribution of energy on a classical system via a generalized Langevin thermostat and provides computationally affordable and accurate (though approximate) NQEs. We discuss some implementation details, efficient numerical schemes, and parallelization strategies and quickly review the GPU acceleration of our code. Our implementation allows an efficient inclusion of NQEs in MD simulations for very large systems, as demonstrated by scaling tests on water boxes with more than 200,000 atoms (simulated using the AMOEBA polarizable force field). We test the compatibility of the approach with Tinker-HP's recently introduced Deep-HP machine learning potentials module by computing water properties using the DeePMD potential with adQTB thermostatting. Finally, we show that the platform is also compatible with the alchemical free energy estimation capabilities of Tinker-HP and fast enough to perform simulations. Therefore, we study how NQEs affect the hydration free energy of small molecules solvated with the recently developed Q-AMOEBA water force field. Overall, the Quantum-HP platform allows users to perform routine quantum MD simulations of large condensed-phase systems and will help to shed new light on the quantum nature of important interactions in biological matter.
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Affiliation(s)
- Thomas Plé
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Nastasia Mauger
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | | | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Simon Huppert
- Institut des Nanosciences de Paris (INSP), CNRS UMR 7588, and Sorbonne Université, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France.,Institut Universitaire de France, 75005 Paris, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Mauger N, Plé T, Lagardère L, Huppert S, Piquemal JP. Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field. J Phys Chem B 2022; 126:8813-8826. [PMID: 36270033 DOI: 10.1021/acs.jpcb.2c04454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a ForceBalance fitting strategy including high-level quantum chemistry reference energies and selected condensed-phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas-phase and condensed-phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas-phase equilibrium value, isotope effects, and so on. Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins, and nucleic acids opening the possibility for the large-scale study of the importance of NQEs in biophysics.
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Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
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5
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Stenqvist B, Aspelin V, Lund M. Generalized Moment Correction for Long-Ranged Electrostatics. J Chem Theory Comput 2020; 16:3737-3745. [PMID: 32315176 PMCID: PMC7588037 DOI: 10.1021/acs.jctc.9b01003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Describing
long-ranged electrostatics using short-ranged pair potentials
is appealing because the computational complexity scales linearly
with the number of particles. The foundation of the approach presented
here is to mimic the long-ranged medium response by cancelling electric
multipoles within a small cutoff sphere. We propose a rigorous and
formally exact new method that cancels up to infinitely many multipole moments and is free of operational damping parameters
often required in existing theories. Using molecular dynamics simulations
of water with and without added salt, we discuss radial distribution
functions, Kirkwood–Buff integrals, dielectrics, diffusion
coefficients, and angular correlations in relation to existing electrostatic
models. We find that the proposed method is an efficient and accurate
alternative for handling long-ranged electrostatics as compared to
Ewald summation schemes. The methodology and proposed parameterization
are applicable also for dipole–dipole interactions.
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Affiliation(s)
- Björn Stenqvist
- Division of Physical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden.,Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vidar Aspelin
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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6
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Ko HY, Zhang L, Santra B, Wang H, E W, DiStasio Jr RA, Car R. Isotope effects in liquid water via deep potential molecular dynamics. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1652366] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Biswajit Santra
- Department of Physics, Temple University, Philadelphia, PA, USA
| | - Han Wang
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Beijing, People's Republic of China
| | - Weinan E
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
- Department of Mathematics, Princeton University, Princeton, NJ, USA
| | | | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
- Department of Physics and Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, NJ, USA
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7
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8
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Stenqvist B, Lund M. On short-ranged pair-potentials for long-range electrostatics. Phys Chem Chem Phys 2019; 21:24787-24792. [DOI: 10.1039/c9cp03875b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fast and accurate summation of long-range electrostatics by using a short-ranged pair-potential that ensures moment cancellation in the cutoff sphere.
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Affiliation(s)
- Björn Stenqvist
- Division of Physical Chemistry
- Lund University
- SE-22100 Lund
- Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry
- Lund University
- SE-22100 Lund
- Sweden
- LINXS – Lund Institute of Advanced Neutron and X-ray Science
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9
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Elton DC, Fritz M, Fernández-Serra M. Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost. Phys Chem Chem Phys 2018; 21:409-417. [PMID: 30534683 DOI: 10.1039/c8cp06077k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy. The method is based on the many body expansion of the energy and has the benefit of including a monomer level correction to the DFT energy. Our method calculates intramolecular forces using the highly accurate monomer potential energy surface developed by Partridge-Schwenke, which is cheap to evaluate. Intermolecular forces and energies are calculated with DFT only once per timestep using the centroid positions. We show how our method may be used in conjunction with a multiple time step algorithm for an additional speedup and how it relates to ring polymer contraction and other schemes that have been introduced recently to speed up PIMD simulations. We show that our method, which we call "monomer PIMD", correctly captures changes in the structure of water found in a full PIMD simulation but at much lower computational cost.
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Affiliation(s)
- Daniel C Elton
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA.
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10
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11
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Buxton SJ, Habershon S. Accelerated path-integral simulations using ring-polymer interpolation. J Chem Phys 2017; 147:224107. [DOI: 10.1063/1.5006465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Samuel J. Buxton
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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12
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Hamm P, Fanourgakis GS, Xantheas SS. A surprisingly simple correlation between the classical and quantum structural networks in liquid water. J Chem Phys 2017; 147:064506. [DOI: 10.1063/1.4993166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - George S. Fanourgakis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, P.O. Box 2208, 70013 Heraklion, Greece
| | - Sotiris S. Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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13
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Mouhat F, Sorella S, Vuilleumier R, Saitta AM, Casula M. Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics. J Chem Theory Comput 2017; 13:2400-2417. [DOI: 10.1021/acs.jctc.7b00017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Félix Mouhat
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Sandro Sorella
- International
School for Advanced Studies (SISSA), Via Bonomea 26, 34136 Trieste, Italy
- INFM Democritos
National Simulation Center, 34151 Trieste, Italy
| | - Rodolphe Vuilleumier
- PASTEUR,
Département de chimie, École normale supérieure,
UPMC Univ Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, École normale supérieure, CNRS, Processus d’activation
sélective par transfert d’énergie uni-électronique
ou radiatif (PASTEUR), 75005 Paris, France
| | - Antonino Marco Saitta
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Michele Casula
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
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14
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Marsalek O, Markland TE. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects. J Phys Chem Lett 2017; 8:1545-1551. [PMID: 28296422 DOI: 10.1021/acs.jpclett.7b00391] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to 2 orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infrared and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.
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Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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15
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Agarwal A, Clementi C, Delle Site L. Path integral-GC-AdResS simulation of a large hydrophobic solute in water: a tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Phys Chem Chem Phys 2017; 19:13030-13037. [DOI: 10.1039/c7cp01629h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We perform large scale quantum (path integral) molecular dynamics simulations of a C60 -like molecule in water.
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16
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Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chem Rev 2016; 116:7529-50. [DOI: 10.1021/acs.chemrev.5b00674] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Wei Fang
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Peter G. Kusalik
- Department
of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ross H. McKenzie
- School
of Mathematics and Physics, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Angelos Michaelides
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
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17
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Cheng X, Herr JD, Steele RP. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping. J Chem Theory Comput 2016; 12:1627-38. [DOI: 10.1021/acs.jctc.6b00021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaolu Cheng
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jonathan D. Herr
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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18
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Marsalek O, Markland TE. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory. J Chem Phys 2016; 144:054112. [DOI: 10.1063/1.4941093] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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19
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20
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Agarwal A, Delle Site L. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water. J Chem Phys 2015; 143:094102. [DOI: 10.1063/1.4929738] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Animesh Agarwal
- Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Luigi Delle Site
- Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
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21
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Fanourgakis GS. An Extension of Wolf’s Method for the Treatment of Electrostatic Interactions: Application to Liquid Water and Aqueous Solutions. J Phys Chem B 2015; 119:1974-85. [DOI: 10.1021/jp510612w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- George S. Fanourgakis
- Computation-based Science
and Technology Research Center (CaSToRC), The Cyprus Institute, P.O. Box 27456, 1645 Nicosia, Cyprus
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22
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Babbush R, Parkhill J, Aspuru-Guzik A. Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions. Front Chem 2013; 1:26. [PMID: 24790954 PMCID: PMC3982527 DOI: 10.3389/fchem.2013.00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 10/08/2013] [Indexed: 11/13/2022] Open
Abstract
Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory.
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Affiliation(s)
- Ryan Babbush
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridge, MA, USA
| | - John Parkhill
- Department of Chemistry, The University of Notre DameSouth Bend, IN, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridge, MA, USA
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23
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Habershon S, Manolopoulos DE, Markland TE, Miller TF. Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space. Annu Rev Phys Chem 2013; 64:387-413. [DOI: 10.1146/annurev-physchem-040412-110122] [Citation(s) in RCA: 448] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - David E. Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305;
| | - Thomas F. Miller
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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24
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Calvo F, Falvo C, Parneix P. A simple but accurate potential for the naphthalene-argon complex: Applications to collisional energy transfer and matrix isolated IR spectroscopy. J Chem Phys 2013; 138:034305. [DOI: 10.1063/1.4773469] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Ceriotti M, Markland TE. Efficient methods and practical guidelines for simulating isotope effects. J Chem Phys 2013; 138:014112. [DOI: 10.1063/1.4772676] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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26
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Wang LP, Chen J, Van Voorhis T. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data. J Chem Theory Comput 2012; 9:452-60. [PMID: 26589047 DOI: 10.1021/ct300826t] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We introduce ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data. We outline several important challenges in force field development and how they are addressed in ForceBalance, and present an example calculation where these methods are applied to develop a highly accurate polarizable water model. ForceBalance is available for free download at https://simtk.org/home/forcebalance.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, Stanford University, 318 Campus Drive, Stanford, California 94350, United States
| | - Jiahao Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Zeidler A, Salmon PS, Fischer HE, Neuefeind JC, Simonson JM, Markland TE. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284126. [PMID: 22738936 DOI: 10.1088/0953-8984/24/28/284126] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The structures of heavy and light water at 300 K were investigated by using a joint approach in which the method of neutron diffraction with oxygen isotope substitution was complemented by path integral molecular dynamics simulations. The diffraction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) Å, were found to be in best agreement with those obtained by using the flexible anharmonic TTM3-F water model. Both techniques show a difference of ≃ 0.5% between the O-D and O-H intra-molecular bond lengths, and the results support a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.
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Affiliation(s)
- Anita Zeidler
- Department of Physics, University of Bath, Bath BA2 7AY, UK
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Fanourgakis GS, Medina JS, Prosmiti R. Determining the Bulk Viscosity of Rigid Water Models. J Phys Chem A 2012; 116:2564-70. [DOI: 10.1021/jp211952y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - J. S. Medina
- Instituto de Física Fundamental (CSIC), Serrano 123, 28006 Madrid, Spain
| | - R. Prosmiti
- Instituto de Física Fundamental (CSIC), Serrano 123, 28006 Madrid, Spain
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29
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Zeidler A, Salmon PS, Fischer HE, Neuefeind JC, Simonson JM, Lemmel H, Rauch H, Markland TE. Oxygen as a site specific probe of the structure of water and oxide materials. PHYSICAL REVIEW LETTERS 2011; 107:145501. [PMID: 22107211 DOI: 10.1103/physrevlett.107.145501] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Indexed: 05/16/2023]
Abstract
The method of oxygen isotope substitution in neutron diffraction is introduced as a site specific structural probe. It is employed to measure the structure of light versus heavy water, thus circumventing the assumption of isomorphism between H and D as used in more traditional neutron diffraction methods. The intramolecular and intermolecular O-H and O-D pair correlations are in excellent agreement with path integral molecular dynamics simulations, both techniques showing a difference of ≃0.5% between the O-H and O-D intramolecular bond distances. The results support the validity of a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intramolecular and intermolecular quantum contributions.
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Affiliation(s)
- Anita Zeidler
- Department of Physics, University of Bath, Bath, BA2 7AY, United Kingdom
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30
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Sala J, Guàrdia E, Masia M. The polarizable point dipoles method with electrostatic damping: implementation on a model system. J Chem Phys 2011; 133:234101. [PMID: 21186852 DOI: 10.1063/1.3511713] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water.
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Affiliation(s)
- Jonàs Sala
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain.
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Ceriotti M, Manolopoulos DE, Parrinello M. Accelerating the convergence of path integral dynamics with a generalized Langevin equation. J Chem Phys 2011; 134:084104. [PMID: 21361524 DOI: 10.1063/1.3556661] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michele Ceriotti
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, Lugano, Switzerland.
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32
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Steele RP, Zwickl J, Shushkov P, Tully JC. Mixed time slicing in path integral simulations. J Chem Phys 2011; 134:074112. [DOI: 10.1063/1.3518714] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Vega C, Abascal JLF. Simulating water with rigid non-polarizable models: a general perspective. Phys Chem Chem Phys 2011; 13:19663-88. [DOI: 10.1039/c1cp22168j] [Citation(s) in RCA: 658] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shaik MS, Liem SY, Popelier PLA. Properties of liquid water from a systematic refinement of a high-rank multipolar electrostatic potential. J Chem Phys 2010; 132:174504. [PMID: 20459171 DOI: 10.1063/1.3409563] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We build on previous work [S. Y. Liem and P. L. A. Popelier, J. Chem. Theory Comput. 4, 353 (2008)], where for the first time, a high-rank multipolar electrostatic potential was used in molecular dynamics simulations of liquid water at a wide range of pressures and temperatures, and using a multipolar Ewald summation. Water is represented as a rigid body, with atomic multipole moments defined by quantum chemical topology partitioning its gas phase electron density. The effect of the level of theory on the local structure of liquid water is systematically addressed. Values for Lennard-Jones (LJ) parameters are optimized, for both oxygen and hydrogen atoms, against bulk properties. The best LJ parameters were then used in a set of simulations at 30 different temperatures (1 atm) and another set at 11 different pressures (at 298 K). Inclusion of the hydrogen LJ parameters significantly increases the self-diffusion coefficient. The behavior of bulk properties was studied and the local water structure analyzed by both radial and spatial distribution functions. Comparisons with familiar point-charge potentials, such as TIP3P, TIP4P, TIP5P, and simple point charge, show the benefits of multipole moments.
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Affiliation(s)
- Majeed S Shaik
- Manchester Interdisciplinary Biocentre (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Conde MM, Vega C, McBride C, Noya EG, Ramírez R, Sesé LM. Can gas hydrate structures be described using classical simulations? J Chem Phys 2010; 132:114503. [DOI: 10.1063/1.3353953] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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36
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González BS, Noya EG, Vega C, Sesé LM. Nuclear Quantum Effects in Water Clusters: The Role of the Molecular Flexibility. J Phys Chem B 2010; 114:2484-92. [DOI: 10.1021/jp910770y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Briesta S. González
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eva G. Noya
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Luis M. Sesé
- Departamento Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, UNED, Paseo Senda del Rey 9, 28040 Madrid, Spain
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Habershon S, Manolopoulos DE. Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water. J Chem Phys 2009; 131:244518. [DOI: 10.1063/1.3276109] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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