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Plé T, Lagardère L, Piquemal JP. Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects. Chem Sci 2023; 14:12554-12569. [PMID: 38020379 PMCID: PMC10646944 DOI: 10.1039/d3sc02581k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
We introduce FENNIX (Force-Field-Enhanced Neural Network InteraXions), a hybrid approach between machine-learning and force-fields. We leverage state-of-the-art equivariant neural networks to predict local energy contributions and multiple atom-in-molecule properties that are then used as geometry-dependent parameters for physically-motivated energy terms which account for long-range electrostatics and dispersion. Using high-accuracy ab initio data (small organic molecules/dimers), we trained a first version of the model. Exhibiting accurate gas-phase energy predictions, FENNIX is transferable to the condensed phase. It is able to produce stable Molecular Dynamics simulations, including nuclear quantum effects, for water predicting accurate liquid properties. The extrapolating power of the hybrid physically-driven machine learning FENNIX approach is exemplified by computing: (i) the solvated alanine dipeptide free energy landscape; (ii) the reactive dissociation of small molecules.
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Affiliation(s)
- Thomas Plé
- Sorbonne Université, LCT, UMR 7616 CNRS F-75005 Paris France thomas.ple@sorbonne-université louis.lagardere@sorbonne-université jean-philip.piquemal@sorbonne-université
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS F-75005 Paris France thomas.ple@sorbonne-université louis.lagardere@sorbonne-université jean-philip.piquemal@sorbonne-université
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS F-75005 Paris France thomas.ple@sorbonne-université louis.lagardere@sorbonne-université jean-philip.piquemal@sorbonne-université
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Jaffrelot Inizan T, Plé T, Adjoua O, Ren P, Gökcan H, Isayev O, Lagardère L, Piquemal JP. Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects. Chem Sci 2023; 14:5438-5452. [PMID: 37234902 PMCID: PMC10208042 DOI: 10.1039/d2sc04815a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/03/2023] [Indexed: 07/28/2023] Open
Abstract
Deep-HP is a scalable extension of the Tinker-HP multi-GPU molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Network (DNN) models. Deep-HP increases DNNs' MD capabilities by orders of magnitude offering access to ns simulations for 100k-atom biosystems while offering the possibility of coupling DNNs to any classical (FFs) and many-body polarizable (PFFs) force fields. It allows therefore the introduction of the ANI-2X/AMOEBA hybrid polarizable potential designed for ligand binding studies where solvent-solvent and solvent-solute interactions are computed with the AMOEBA PFF while solute-solute ones are computed by the ANI-2X DNN. ANI-2X/AMOEBA explicitly includes AMOEBA's physical long-range interactions via an efficient Particle Mesh Ewald implementation while preserving ANI-2X's solute short-range quantum mechanical accuracy. The DNN/PFF partition can be user-defined allowing for hybrid simulations to include key ingredients of biosimulation such as polarizable solvents, polarizable counter ions, etc.… ANI-2X/AMOEBA is accelerated using a multiple-timestep strategy focusing on the model's contributions to low-frequency modes of nuclear forces. It primarily evaluates AMOEBA forces while including ANI-2X ones only via correction-steps resulting in an order of magnitude acceleration over standard Velocity Verlet integration. Simulating more than 10 μs, we compute charged/uncharged ligand solvation free energies in 4 solvents, and absolute binding free energies of host-guest complexes from SAMPL challenges. ANI-2X/AMOEBA average errors are discussed in terms of statistical uncertainty and appear in the range of chemical accuracy compared to experiment. The availability of the Deep-HP computational platform opens the path towards large-scale hybrid DNN simulations, at force-field cost, in biophysics and drug discovery.
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Affiliation(s)
- Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
| | - Hatice Gökcan
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique FR 2622 CNRS Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
The Wigner thermal density is a function of considerable interest in the area of approximate (linearized or semiclassical) quantum dynamics where it is employed to generate initial conditions for the propagation of appropriate sets of classical trajectories. In this paper, we propose an original approach to compute the Wigner density based on a generalized Langevin equation. The stochastic dynamics is nontrivial in that it contains a coordinate-dependent friction coefficient and a generalized force that couples momenta and coordinates. These quantities are, in general, not known analytically and have to be estimated via auxiliary calculations. The performance of the new sampling scheme is tested on standard model systems with highly nonclassical features such as relevant zero point energy effects, correlation between momenta and coordinates, and negative parts of the Wigner density. In its current brute force implementation, the algorithm, whose convergence can be systematically checked, is accurate and has only limited overhead compared to schemes with similar characteristics. We briefly discuss potential ways to further improve its numerical efficiency.
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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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Mangaud E, Huppert S, Plé T, Depondt P, Bonella S, Finocchi F. The Fluctuation–Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations. J Chem Theory Comput 2019; 15:2863-2880. [DOI: 10.1021/acs.jctc.8b01164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Etienne Mangaud
- Sorbonne Université, CNRS - UMR 7588, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, CNRS - UMR 7588, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, CNRS - UMR 7588, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Philippe Depondt
- Sorbonne Université, CNRS - UMR 7588, 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
| | - Fabio Finocchi
- Sorbonne Université, CNRS - UMR 7588, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
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