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Kieninger S, Keller BG. GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J Chem Theory Comput 2022; 18:5792-5798. [DOI: 10.1021/acs.jctc.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefanie Kieninger
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
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2
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He X, Wu B, Shang Y, Li B, Cheng X, Liu J. New phase space formulations and quantum dynamics approaches. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xin He
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Baihua Wu
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Youhao Shang
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Bingqi Li
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Xiangsong Cheng
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
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3
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Simulation of Nuclear Quantum Effects in Condensed Matter Systems via Quantum Baths. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This paper reviews methods that aim at simulating nuclear quantum effects (NQEs) using generalized thermal baths. Generalized (or quantum) baths simulate statistical quantum features, and in particular zero-point energy effects, through non-Markovian stochastic dynamics. They make use of generalized Langevin Equations (GLEs), in which the quantum Bose–Einstein energy distribution is enforced by tuning the random and friction forces, while the system degrees of freedom remain classical. Although these baths have been formally justified only for harmonic oscillators, they perform well for several systems, while keeping the cost of the simulations comparable to the classical ones. We review the formal properties and main characteristics of classical and quantum GLEs, in relation with the fluctuation–dissipation theorems. Then, we describe the quantum thermostat and quantum thermal bath, the two generalized baths currently most used, providing several examples of applications for condensed matter systems, including the calculation of vibrational spectra. The most important drawback of these methods, zero-point energy leakage, is discussed in detail with the help of model systems, and a recently proposed scheme to monitor and mitigate or eliminate it—the adaptive quantum thermal bath—is summarised. This approach considerably extends the domain of application of generalized baths, leading, for instance, to the successful simulation of liquid water, where a subtle interplay of NQEs is at play. The paper concludes by overviewing further development opportunities and open challenges of generalized baths.
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4
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Poulsen JA, Nyman G. A Divergence-Free Wigner Transform of the Boltzmann Operator Based on an Effective Frequency Theory. J Phys Chem A 2021; 125:9209-9225. [PMID: 34636560 PMCID: PMC8543443 DOI: 10.1021/acs.jpca.1c05860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
The centroid effective
frequency representation of path integrals
as developed by Feynman and Kleinert was originally aimed at calculating
partition functions and related quantities in the canonical ensemble.
In its path integral formulation, only closed paths
were relevant. This formulation has been used by the present authors
in order to calculate the many-body Wigner function of the Boltzmann
operator, which includes also open paths. This usage of the theory
outside of the original intention can lead to mathematical divergence
issues for potentials with barriers, particularly at low temperature.
In the present paper, we modify the effective frequency theory of
Feynman and Kleinert by also including open paths in its variational
equations. In this way, a divergence-free approximation to the Boltzmann
operator matrix elements is derived. This generalized version of Feynman
and Kleinert’s formulation is thus more robust and can be applied
to all types of barriers at all temperatures. This new version is
used to calculate the Wigner functions of the Boltzmann operator for
a quartic oscillator and for a double well potential and both static
and dynamic properties are studied at several temperatures. The new
theory is found to be essentially as precise as the original one.
Its advantage is that it will always deliver a well-defined, even
if approximate, Wigner function, which can, for instance, be used
for sampling initial conditions for molecular dynamics simulations.
As will be discussed, the theory can be systematically improved by
including higher-order Fourier modes into the nonquadratic part of
the trial action.
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Affiliation(s)
- Jens Aage Poulsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30 Gothenburg, Sweden
| | - Gunnar Nyman
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30 Gothenburg, Sweden
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5
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Plé T, Huppert S, Finocchi F, Depondt P, Bonella S. Anharmonic spectral features via trajectory-based quantum dynamics: A perturbative analysis of the interplay between dynamics and sampling. J Chem Phys 2021; 155:104108. [PMID: 34525824 DOI: 10.1063/5.0056824] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The performance of different approximate algorithms for computing anharmonic features in vibrational spectra is analyzed and compared on model and more realistic systems that present relevant nuclear quantum effects. The methods considered combine approximate sampling of the quantum thermal distribution with classical time propagation and include Matsubara dynamics, path integral dynamics approaches, linearized initial value representation, and the recently introduced adaptive quantum thermal bath. A perturbative analysis of these different methods enables us to account for the observed numerical performance on prototypes for overtones and combination bands and to draw qualitatively correct trends for the numerical results obtained for Fermi resonances. Our results prove that the unequal performances of these approaches often derive from the method employed to sample initial conditions and not, as usually assumed, from the lack of coherence in the time propagation. Furthermore, as confirmed by the analysis reported in Benson and Althorpe, J. Chem. Phys. 130, 194510 (2021), we demonstrate, both via the perturbative approach and numerically, that path integral dynamics methods fail to reproduce the intensities of these anharmonic features and follow purely classical trends with respect to their temperature behavior. Finally, the remarkably accurate performance of the adaptive quantum thermal bath approach is documented and motivated.
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Affiliation(s)
- Thomas Plé
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Fabio Finocchi
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Philippe Depondt
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
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6
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Mauger N, Plé T, Lagardère L, Bonella S, Mangaud É, Piquemal JP, Huppert S. Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath. J Phys Chem Lett 2021; 12:8285-8291. [PMID: 34427440 DOI: 10.1021/acs.jpclett.1c01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQEs) in molecular simulations: the adaptive quantum thermal bath (adQTB). In this method, zero-point energy is introduced through a generalized Langevin thermostat designed to precisely enforce the quantum fluctuation-dissipation theorem. We propose a refined adQTB algorithm with improved accuracy and report adQTB simulations of liquid water. Through extensive comparison with reference path integral calculations, we demonstrate that it provides excellent accuracy for a broad range of structural and thermodynamic observables as well as infrared vibrational spectra. The adQTB has a computational cost comparable to that of classical molecular dynamics, enabling simulations of up to millions of degrees of freedom.
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Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Thomas Plé
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - Étienne Mangaud
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, 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
| | - Simon Huppert
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
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Pieroni C, Marsili E, Lauvergnat D, Agostini F. Relaxation dynamics through a conical intersection: Quantum and quantum-classical studies. J Chem Phys 2021; 154:034104. [PMID: 33499611 DOI: 10.1063/5.0036726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We study the relaxation process through a conical intersection of a photo-excited retinal chromophore model. The analysis is based on a two-electronic-state two-dimensional Hamiltonian developed by Hahn and Stock [J. Phys. Chem. B 104 1146 (2000)] to reproduce, with a minimal model, the main features of the 11-cis to all-trans isomerization of the retinal of rhodopsin. In particular, we focus on the performance of various trajectory-based schemes to nonadiabatic dynamics, and we compare quantum-classical results to the numerically exact quantum vibronic wavepacket dynamics. The purpose of this work is to investigate, by analyzing electronic and nuclear observables, how the sampling of initial conditions for the trajectories affects the subsequent dynamics.
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Affiliation(s)
- Carlotta Pieroni
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Emanuele Marsili
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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