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Gresh N, El Hage K, Lagardère L, Brégier F, Godard J, Piquemal JP, Perrée-Fauvet M, Sol V. Enforcing Local DNA Kinks by Sequence-Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study. Chemphyschem 2024; 25:e202300776. [PMID: 38088522 DOI: 10.1002/cphc.202300776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/24/2023] [Indexed: 02/03/2024]
Abstract
Bisacridinyl-bisarginyl porphyrin (BABAP) is a trisintercalating derivative of a tricationic porphyrin, formerly designed and synthesized in order to selectively target and photosensitize the ten-base pair palindromic sequence d(CGGGCGCCCG)2 . We resorted to the previously derived (Far et al., 2004) lowest energy-minimized (EM) structure of the BABAP complex with this sequence as a starting point. We performed polarizable molecular dynamics (MD) on this complex. It showed, over a 150 ns duration, the persistent binding of the Arg side-chain on each BABAP arm to the two G bases upstream from the central porphyrin intercalation site. We subsequently performed progressive shortenings of the connector chain linking the Arg-Gly backbone to the acridine, from n=6 methylenes to 4, followed by removal of the Gly backbone and further connector shortenings, from n=4 to n=1. These resulted into progressive deformations ('kinks') of the DNA backbone. In its most accented kinked structure, the DNA backbone was found to have a close overlap with that of DNA bound to Cre recombinase, with, at the level of one acridine intercalation site, negative roll and positive tilt values consistent with those experimentally found for this DNA at its own kinked dinucleotide sequence. Thus, in addition to their photosensitizing properties, some BABAP derivatives could induce sequence-selective, controlled DNA deformations, which are targets for cleavage by endonucleases or for repair enzymes.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | - Krystel El Hage
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | | | - Jérémy Godard
- LABCiS UR22722, Univ. Limoges, F-87000, Limoges, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | | | - Vincent Sol
- LABCiS UR22722, Univ. Limoges, F-87000, Limoges, France
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2
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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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3
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Poier PP, Lagardère L, Piquemal JP. Smooth particle mesh Ewald-integrated stochastic Lanczos many-body dispersion algorithm. J Chem Phys 2023; 159:154109. [PMID: 37861116 DOI: 10.1063/5.0166476] [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] [Received: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this formulation, which is only possible due to the Stochastic Lanczos' reliance on matrix-vector products, introduces generalized dipoles and fields. These key quantities allow for a state-of-the-art treatment of periodic boundary conditions via the O(Nlog(N)) Smooth Particle Mesh Ewald (SPME) approach which uses efficient fast Fourier transforms. This SPME-Lanczos algorithm drastically outperforms the standard replica method which is affected by a slow and conditionally convergence rate that limits an efficient and reliable inclusion of long-range periodic boundary conditions interactions in many-body dispersion modelling. The proposed algorithm inherits the embarrassingly parallelism of the original Stochastic Lanczos scheme, thus opening up for a fully converged and efficient periodic boundary conditions treatment of MBD approaches.
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Affiliation(s)
- Pier Paolo Poier
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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4
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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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Chollet I, Lagardère L, Piquemal JP. ANKH: A Generalized O( N) Interpolated Ewald Strategy for Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:2887-2905. [PMID: 37134146 DOI: 10.1021/acs.jctc.3c00015] [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: 05/05/2023]
Abstract
To evaluate electrostatics interactions, molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM) approaches. However, the FFTs low scalability remains a strong bottleneck for large-scale PME simulations on supercomputers. On the opposite, FFT-free FMM techniques are able to deal efficiently with such systems but they fail to reach PME performances for small- to medium-size systems, limiting their real-life applicability. We propose ANKH, a strategy grounded on interpolated Ewald summations and designed to remain efficient/scalable for any size of systems. The method is generalized for distributed point multipoles, and so for induced dipoles, which makes it suitable for high performance simulations using new generation polarizable force fields toward exascale computing.
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Affiliation(s)
- Igor Chollet
- LAGA, Université Sorbonne Paris Nord, UMR 7539, Villetaneuse, France and LCT, Sorbonne Université, UMR 7616, Paris, 75006, France
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6
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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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7
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Poier PP, Adjoua O, Lagardère L, Piquemal JP. Generalized Many-Body Dispersion Correction through Random-Phase Approximation for Chemically Accurate Density Functional Theory. J Phys Chem Lett 2023; 14:1609-1617. [PMID: 36749715 PMCID: PMC9940194 DOI: 10.1021/acs.jpclett.2c03722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
We extend our recently proposed Deep Learning-aided many-body dispersion (DNN-MBD) model to quadrupole polarizability (Q) terms using a generalized Random Phase Approximation (RPA) formalism, thus enabling the inclusion of van der Waals contributions beyond dipole. The resulting DNN-MBDQ model only relies on ab initio-derived quantities as the introduced quadrupole polarizabilities are recursively retrieved from dipole ones, in turn modeled via the Tkatchenko-Scheffler method. A transferable and efficient deep-neuronal network (DNN) provides atom-in-molecule volumes, while a single range-separation parameter is used to couple the model to Density Functional Theory (DFT). Since it can be computed at a negligible cost, the DNN-MBDQ approach can be coupled with DFT functionals, such as PBE, PBE0, and B86bPBE (dispersionless). The DNN-MBQ-corrected functionals reach chemical accuracy while exhibiting lower errors compared to their dipole-only counterparts.
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Affiliation(s)
| | - Olivier Adjoua
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
| | - Louis Lagardère
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
- Sorbonne
Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
- The
University of Texas at Austin, Department
of Biomedical Engineering, Austin, Texas 78712, United States
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8
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El Hage K, Ribaudo G, Lagardère L, Ongaro A, Kahn PH, Demange L, Piquemal JP, Zagotto G, Gresh N. Targeting the Major Groove of the Palindromic d(GGCGCC) 2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. J Chem Inf Model 2022; 62:6649-6666. [PMID: 35895094 DOI: 10.1021/acs.jcim.2c00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)2 sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O6/N7 of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N9-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C1G2G3G4C5G6C7C8C9G10)2. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.
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Affiliation(s)
- Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91000 Evry, France
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | - Louis Lagardère
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
| | - Alberto Ongaro
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | | | - Luc Demange
- Université Paris Cité, CiTCoM, UMR 8038 CNRS, 75006 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France.,The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas 78705, United States
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo, 35131 Padova, Italy
| | - Nohad Gresh
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
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9
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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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10
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Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
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Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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11
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Poier PP, Jaffrelot Inizan T, Adjoua O, Lagardère L, Piquemal JP. Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory. J Phys Chem Lett 2022; 13:4381-4388. [PMID: 35544748 DOI: 10.1021/acs.jpclett.2c00936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using a deep neuronal network (DNN) model trained on the large ANI-1 data set of small organic molecules, we propose a transferable density-free many-body dispersion (DNN-MBD) model. The DNN strategy bypasses the explicit Hirshfeld partitioning of the Kohn-Sham electron density required by MBD models to obtain the atom-in-molecules volumes used by the Tkatchenko-Scheffler polarizability rescaling. The resulting DNN-MBD model is trained with minimal basis iterative Stockholder atomic volumes and, coupled to density functional theory (DFT), exhibits comparable (if not greater) accuracy to other approaches based on different partitioning schemes. Implemented in the Tinker-HP package, the DNN-MBD model decreases the overall computational cost compared to MBD models where the explicit density partitioning is performed. Its coupling with the recently introduced Stochastic formulation of the MBD equations (J. Chem. Theory Comput. 2022, 18 (3), 1633-1645) enables large routine dispersion-corrected DFT calculations at preserved accuracy. Furthermore, the DNN electron density-free features extend the MBD model's applicability beyond electronic structure theory within methodologies such as force fields and neural networks.
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Affiliation(s)
| | | | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, Paris 75005, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78713, United States
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12
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El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hédin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturlese M, Sosic A, Volpiana M, Lugato A, Barone M, Gatto B, Macchia ML, Bellanda M, Battistutta R, Salata C, Kondratov I, Iminov R, Khairulin A, Mykhalonok Y, Pochepko A, Chashka-Ratushnyi V, Kos I, Moro S, Montes M, Ren P, Ponder JW, Lagardère L, Piquemal JP, Sabbadin D. Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation. Chem Sci 2022; 13:3674-3687. [PMID: 35432906 PMCID: PMC8966641 DOI: 10.1039/d1sc05892d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease (Mpro) inhibitors whose potency ranges from mM for the initial non-covalent ligands to sub-μM for the final covalent compound (IC50 = 830 ± 50 nM). The project extensively relied on high-resolution all-atom molecular dynamics simulations and absolute binding free energy calculations performed using the polarizable AMOEBA force field. The study is complemented by extensive adaptive sampling simulations that are used to rationalize the different ligand binding poses through the explicit reconstruction of the ligand–protein conformation space. Machine learning predictions are also performed to predict selected compound properties. While simulations extensively use high performance computing to strongly reduce the time-to-solution, they were systematically coupled to nuclear magnetic resonance experiments to drive synthesis and for in vitro characterization of compounds. Such a study highlights the power of in silico strategies that rely on structure-based approaches for drug design and allows the protein conformational multiplicity problem to be addressed. The proposed fluorinated tetrahydroquinolines open routes for further optimization of Mpro inhibitors towards low nM affinities. The dominant binding mode of the QUB-00006-Int-07 main protease inhibitor during absolute binding free energy simulations.![]()
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Affiliation(s)
- Léa El Khoury
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Zhifeng Jing
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Alberto Cuzzolin
- Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche Largo Belloli 11a 43122 Parma Italy
| | - Alessandro Deplano
- Pharmacelera, Torre R, 4a planta Despatx A05, Parc Cientific de Barcelona, Baldiri Reixac 8 08028 Barcelona Spain
| | - Daniele Loco
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Boris Sattarov
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Florent Hédin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of LifeSciences Hofackerstrasse 30 CH-4132 Muttenz Switzerland
| | - Chris Ho
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Dina El Ahdab
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Theo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Martina Volpiana
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Angela Lugato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Marco Barone
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Maria Ludovica Macchia
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Massimo Bellanda
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Roberto Battistutta
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua via Gabelli 63 35121 Padova Italy
| | | | - Rustam Iminov
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | | | | | | | | | - Iaroslava Kos
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Matthieu Montes
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université 2 Rue Conte 75003 Paris France
| | - Pengyu Ren
- University of Texas at Austin, Department of Biomedical Engineering TX 78712 USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis MO 63130 USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine MO 63110 USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France .,Institut Universitaire de France 75005 Paris France
| | - Davide Sabbadin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
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13
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Abstract
We propose a new strategy to solve the key equations of the many-body dispersion (MBD) model by Tkatchenko, DiStasio Jr., and Ambrosetti. Our approach overcomes the original O(N3) computational complexity that limits its applicability to large molecular systems within the context of O(N) density functional theory. First, to generate the required frequency-dependent screened polarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reduces the number of variables and, coupled to a direct inversion of the iterative subspace extrapolation, exhibits linear-scaling performances. Second, we apply a stochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantum harmonic oscillators. While scaling linearly, it also enables communication-free pleasingly parallel implementations. As the resulting O(N) stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms' complex materials and solvated biosystems with computational times in the range of minutes.
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Affiliation(s)
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75052, France.,IP2CT, FR 2622 CNRS, Sorbonne Université, Paris 75005, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75052, France.,Institut Universitaire de France, Paris 75231, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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14
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Célerse F, Inizan TJ, Lagardère L, Adjoua O, Monmarché P, Miao Y, Derat E, Piquemal JP. An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems. J Chem Theory Comput 2022; 18:968-977. [PMID: 35080892 DOI: 10.1021/acs.jctc.1c01024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups, thanks to the use of fast multiple-time step integrators. To further reduce the time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD─US/dual-water approach is tested on the 1D Potential of Mean Force (PMF) of the solvated CD2-CD58 system (168 000 atoms), allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added, enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling-US-GaMD (ASUS-GaMD) scheme. The highly parallel ASUS-GaMD setup decreases time to convergence by, respectively, 10 and 20 times, compared to GaMD-US and US. Overall, beside the acceleration of PMF computations, Tinker-HP now allows for the simultaneous use of Adaptive Sampling and GaMD-"dual water" enhanced sampling approaches increasing the applicability of polarizable force fields to large-scale simulations of biological systems.
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Affiliation(s)
- Frédéric Célerse
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75005, France.,IPCM, UMR 8232 CNRS, Sorbonne Université, Paris 75005, France
| | | | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75005, France.,IP2CT, FR 2622 CNRS, Sorbonne Université, Paris 75005, France
| | - Olivier Adjoua
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75005, France
| | - Pierre Monmarché
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75005, France.,LJLL, UMR 7598 CNRS, Sorbonne Université, Paris 75005, France
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Etienne Derat
- IPCM, UMR 8232 CNRS, Sorbonne Université, Paris 75005, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75005, France.,The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas 78705, United States.,Institut Universitaire de France, Paris 75005, France
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15
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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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16
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El Ahdab D, Lagardère L, Inizan TJ, Célerse F, Liu C, Adjoua O, Jolly LH, Gresh N, Hobaika Z, Ren P, Maroun RG, Piquemal JP. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. J Phys Chem Lett 2021; 12:6218-6226. [PMID: 34196568 PMCID: PMC8262171 DOI: 10.1021/acs.jpclett.1c01460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/10/2021] [Indexed: 05/27/2023]
Abstract
Following our previous work ( Chem. Sci. 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy because they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physicochemical microenvironments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.
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Affiliation(s)
- Dina El Ahdab
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | | | - Fréderic Célerse
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IPCM, UMR 8232 CNRS, 75005 Paris, France
| | - Chengwen Liu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Zeina Hobaika
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Richard G Maroun
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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17
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Abstract
The computational modeling of realistic extended systems, relevant in, e.g., Chemistry and Biophysics, is a fundamental problem of paramount importance in contemporary research. Enzymatic catalysis and photoinduced processes in pigment-protein complexes are typical problems targeted by computer-aided approaches, to complement experiments as interpretative tools at a molecular scale. The daunting complexity of this task lies in between the opposite stringent requirements of results' reliability for structural/dynamical properties and related intermolecular interactions, and a mandatory principle of realism in the modeling strategy. Therefore, in practice, a truly realistic computational model of a biologically relevant system can easily fail to meet the accuracy requirement, in order to balance the excessive computational cost necessary to reach the desired precision.To address such an "accuracy vs reality" dualistic requirement, mixed quantum mechanics/classical mechanics approaches within Atomistic (i.e., preserving the discrete particle configuration) Polarizable Embeddings (QM/APEs) methods have been proposed over the years. In this Account, we review recent developments in the design and application of general QM/APE methods, targeting situations where a local intrinsically quantum behavior is coupled to a large molecular system (i.e., an environment), often involving processes with different dynamical time scales, in order to avoid brute-force, unpractical quantum chemistry calculations on the complete system.In the first place, our interest is devoted to the available APEs models presently implemented in computational software, highlighting the quantum chemistry methods that can be used to treat the QM subsystem. We review the coupling strategy between the QM subsystem and the APE, which requires to examine the way the QM/MM mutual interactions are accounted for and how the polarization of the classical environment is considered with respect to (wrt) the quantum variables. Because of the need of reliable molecular and macromolecular structures, a pivotal aspect to address here is the handling of the system dynamics (i.e., gradients wrt nuclear positions are required), especially for large molecular assemblies composed by an overwhelming number of atoms, exploring many conformations on a complex energy landscape.Alongside, we highlight our views on the necessary steps to take toward more accurate general-purposes and transferable explicit embeddings. The main objective to achieve here is to design a more physically grounded multiscale approach. To do so, one should apply advanced new generation classical models to account for refined induction effects that are able to (i) improve the quality of QM/MM interaction energies; (ii) enhance transferability by avoiding the compulsory partial (or total) reparameterization of the classical model. Moreover, the extension of recent developments originating from the field of advanced classical molecular dynamics (MD) to the realm of QM/APE methods is a key direction to improve both speed and efficiency for the phase space exploration of systems of growing size and complexity.Lastly, we point out specific research topics where an advanced QM/APE dynamics can certainly shed some light. For example, we discuss chemical reactions in "harsh" environments and the case of spectroscopic theoretical modeling where the inclusion of refined environment effects is often mandatory.
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Affiliation(s)
- Daniele Loco
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Intitut
Parisien de Chimie Physique et Théorique, Sorbonne Université, FR 2622 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Institut
Universitaire de France, F-75005 Paris, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
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18
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Célerse F, Lagardère L, Derat E, Piquemal JP. Correction to "Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Nonpolarizable Simulations of Realistic Systems". J Chem Theory Comput 2021; 17:3235-3236. [PMID: 33908765 DOI: 10.1021/acs.jctc.1c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems. J Chem Theory Comput 2021; 17:2034-2053. [PMID: 33755446 PMCID: PMC8047816 DOI: 10.1021/acs.jctc.0c01164] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Indexed: 11/29/2022]
Abstract
We present the extension of the Tinker-HP package (Lagardère, Chem. Sci. 2018, 9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multiple-GPU architectures ranging from research laboratories to modern supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multiprecision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model. Testing various NVIDIA platforms including 2080Ti, 3090, V100, and A100 cards, we provide illustrative benchmarks of the code for single- and multicards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multinode massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics (see https://github.com/TinkerTools/tinker-hp).
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Affiliation(s)
- Olivier Adjoua
- Sorbonne
Université, LCT, UMR 7616
CNRS, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne
Université, LCT, UMR 7616
CNRS, F-75005 Paris, France
- Sorbonne
Université, IP2CT, FR2622 CNRS, F-75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne
Université, IP2CT, FR2622 CNRS, F-75005 Paris, France
| | | | | | | | - Zhi Wang
- Department
of Chemistry, Washington University in Saint
Louis, Saint Louis, Missouri 63110, United
States
| | | | - Frédéric Célerse
- Sorbonne
Université, LCT, UMR 7616
CNRS, F-75005 Paris, France
- Sorbonne
Université, CNRS, IPCM, F-75005 Paris, France
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Department
of Chemistry, Washington University in Saint
Louis, Saint Louis, Missouri 63110, United
States
| | - Jean-Philip Piquemal
- Sorbonne
Université, LCT, UMR 7616
CNRS, F-75005 Paris, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
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20
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Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. ArXiv 2021:arXiv:2011.01207v4. [PMID: 33173801 PMCID: PMC7654869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Revised: 03/03/2021] [Indexed: 06/11/2023]
Abstract
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multi-GPU architectures ranging from research laboratories to modern supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model. Testing various NVIDIA platforms including 2080Ti, 3090, V100 and A100 cards, we provide illustrative benchmarks of the code for single- and multi-cards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multi-node massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics (see https://github.com/TinkerTools/tinker-hp).
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21
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Jaffrelot Inizan T, Célerse F, Adjoua O, El Ahdab D, Jolly LH, Liu C, Ren P, Montes M, Lagarde N, Lagardère L, Monmarché P, Piquemal JP. High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling. Chem Sci 2021; 12:4889-4907. [PMID: 34168762 PMCID: PMC8179654 DOI: 10.1039/d1sc00145k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient phase-space sampling. Accurate statistical properties can be obtained through reweighting. Within this highly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs on supercomputers, reducing exploration time from years to days. This approach is used to tackle the urgent modeling problem of the SARS-CoV-2 Main Protease (Mpro) producing more than 38 μs of all-atom simulations of its apo (ligand-free) dimer using the high-resolution AMOEBA PFF. The first 15.14 μs simulation (physiological pH) is compared to available non-PFF long-timescale simulation data. A detailed clustering analysis exhibits striking differences between FFs, with AMOEBA showing a richer conformational space. Focusing on key structural markers related to the oxyanion hole stability, we observe an asymmetry between protomers. One of them appears less structured resembling the experimentally inactive monomer for which a 6 μs simulation was performed as a basis for comparison. Results highlight the plasticity of the Mpro active site. The C-terminal end of its less structured protomer is shown to oscillate between several states, being able to interact with the other protomer, potentially modulating its activity. Active and distal site volumes are found to be larger in the most active protomer within our AMOEBA simulations compared to non-PFFs as additional cryptic pockets are uncovered. A second 17 μs AMOEBA simulation is performed with protonated His172 residues mimicking lower pH. Data show the protonation impact on the destructuring of the oxyanion loop. We finally analyze the solvation patterns around key histidine residues. The confined AMOEBA polarizable water molecules are able to explore a wide range of dipole moments, going beyond bulk values, leading to a water molecule count consistent with experimental data. Results suggest that the use of PFFs could be critical in drug discovery to accurately model the complexity of the molecular interactions structuring Mpro.
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Affiliation(s)
| | - Frédéric Célerse
- Sorbonne Université, LCT, UMR 7616 CNRS Paris France
- Sorbonne Université, IPCM, UMR 8232 CNRS Paris France
| | | | - Dina El Ahdab
- Sorbonne Université, LCT, UMR 7616 CNRS Paris France
- Université Saint-Joseph de Beyrouth, UR-EGP Faculté des Sciences Lebanon
| | | | - Chengwen Liu
- University of Texas at Austin, Department of Biomedical Engineering Texas USA
| | - Pengyu Ren
- University of Texas at Austin, Department of Biomedical Engineering Texas USA
| | - Matthieu Montes
- Laboratoire GBCM, EA 7528, CNAM, Hésam Université Paris France
| | | | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS Paris France
- Sorbonne Université, IP2CT, FR 2622 CNRS Paris France
| | - Pierre Monmarché
- Sorbonne Université, LCT, UMR 7616 CNRS Paris France
- Sorbonne Université, LJLL, UMR 7598 CNRS Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS Paris France
- University of Texas at Austin, Department of Biomedical Engineering Texas USA
- Institut Universitaire de France Paris France
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22
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Monmarché P, Weisman J, Lagardère L, Piquemal JP. Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations. J Chem Phys 2020; 153:024101. [PMID: 32668932 DOI: 10.1063/5.0005060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time step specific to each atom-atom pair (two-body) interactions. We start by introducing the formalism of the new velocity jump molecular dynamics, ergodic with respect to the canonical measure. We then introduce the new BOUNCE integrator that allows for long-range forces to be evaluated at random and optimal time steps, leading to strong savings in direct space. The accuracy and computational performances of a first BOUNCE implementation dedicated to classical (non-polarizable) force fields are tested in the cases of pure direct-space droplet-like simulations and of periodic boundary conditions (PBC) simulations using Smooth Particle Mesh Ewald method. An analysis of the capability of BOUNCE to reproduce several condensed-phase properties is provided. Since electrostatics and van der Waals two-body contributions are evaluated much less often than with standard integrators using a 1 fs time step, up to a 400% direct-space acceleration is observed. Applying the reversible reference system propagator algorithms [RESPA(1)] to reciprocal-space (many-body) interactions allows BOUNCE-RESPA(1) to maintain large speedups in PBC while maintaining precision. Overall, we show that replacing the BAOAB standard Langevin integrator by the BOUNCE adaptive framework preserves a similar accuracy and leads to significant computational savings.
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Affiliation(s)
- Pierre Monmarché
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, and Laboratoire de Chimie Théorique, UMR 7616 CNRS, F-75005 Paris, France
| | - Jérémy Weisman
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, F-75005 Paris, France
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23
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El Khoury L, Célerse F, Lagardère L, Jolly LH, Derat E, Hobaika Z, Maroun RG, Ren P, Bouaziz S, Gresh N, Piquemal JP. Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations. J Chem Theory Comput 2020; 16:2013-2020. [PMID: 32178519 DOI: 10.1021/acs.jctc.9b01204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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
Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.
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Affiliation(s)
- Léa El Khoury
- LCT, Sorbonne Université, UMR 7616 CNRS, F-75005 Paris, France.,UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut 1107 2050, Lebanon
| | - Frédéric Célerse
- LCT, Sorbonne Université, UMR 7616 CNRS, F-75005 Paris, France.,Sorbonne Université, CNRS, IPCM, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, IP2CT, FR2622 CNRS, F-75005 Paris, France.,Sorbonne Université, ISCD, F-75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne Université, IP2CT, FR2622 CNRS, F-75005 Paris, France
| | - Etienne Derat
- Sorbonne Université, CNRS, IPCM, F-75005 Paris, France
| | - Zeina Hobaika
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut 1107 2050, Lebanon
| | - Richard G Maroun
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut 1107 2050, Lebanon
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, 75270 Paris, France
| | - Nohad Gresh
- LCT, Sorbonne Université, UMR 7616 CNRS, F-75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, Sorbonne Université, UMR 7616 CNRS, F-75005 Paris, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States.,Institut Universitaire de France, 75005 Paris, France
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24
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Poier PP, Lagardère L, Piquemal JP, Jensen F. Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model. J Chem Theory Comput 2019; 15:6213-6224. [DOI: 10.1021/acs.jctc.9b00721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Louis Lagardère
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, 75005, Paris, France
- Sorbonne Université, Institut des Sciences du Calcul et des Données, 75005, Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, 75005, Paris, France
- Sorbonne Université, Institut Universitaire de France, 75005, Paris, France
- University of Texas, Department of Biomedical Engineering, Austin, Texas, United States
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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25
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Loco D, Lagardère L, Cisneros GA, Scalmani G, Frisch M, Lipparini F, Mennucci B, Piquemal JP. Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Chem Sci 2019; 10:7200-7211. [PMID: 31588288 PMCID: PMC6677116 DOI: 10.1039/c9sc01745c] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/08/2019] [Indexed: 12/17/2022] Open
Abstract
Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms).
In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born–Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.
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Affiliation(s)
- Daniele Loco
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ;
| | - Louis Lagardère
- Sorbonne Université , CNRS , Institut Parisien de Chimie Physique et Théorique, IP2CT , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données, ISCD , Paris , France
| | | | | | | | - Filippo Lipparini
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Benedetta Mennucci
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Jean-Philip Piquemal
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ; .,Institut Universitaire de France, IUF , Paris , France.,The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
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26
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Lagardère L, Aviat F, Piquemal JP. Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics. J Phys Chem Lett 2019; 10:2593-2599. [PMID: 31050904 DOI: 10.1021/acs.jpclett.9b00901] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We propose an incremental construction of multi-time-step integrators to accelerate polarizable point dipole molecular dynamics while preserving sampling efficiency. We start by building integrators using frequency-driven splittings of energy terms and a Velocity-Verlet evaluation of the most rapidly varying forces and compare a standard bonded/nonbonded split to a three-group split dividing nonbonded forces (including polarization) into short- and long-range contributions. We then introduce new approaches by coupling these splittings to Langevin dynamics and to Leimkuhler's BAOAB integrator in order to reach larger time steps (6 fs) for long-range forces. We further increase sampling efficiency by (i) accelerating the polarization evaluation using a fast/noniterative truncated conjugate gradient (TCG-1) as a short-range solver and (ii) pushing the outer time step to 10 fs using hydrogen mass repartitioning. The new BAOAB-RESPA1 integrators demonstrate up to a 7-fold acceleration over standard 1 fs (Tinker-HP) integration and reduce the performance gap between polarizable and classical force fields while preserving static and dynamical properties.
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Affiliation(s)
- Louis Lagardère
- Institut Parisien de Chimie Physique et Theorique , Sorbonne Université, FR2622 CNRS , F-75005 Paris , France
- Institut des Sciences du Calcul et des Données , Sorbonne Université , F-75005 Paris , France
| | - Félix Aviat
- Institut des Sciences du Calcul et des Données , Sorbonne Université , F-75005 Paris , France
- Laboratoire de Chimie Théorique , Sorbonne Université, UMR 7616 CNRS , F-75005 Paris , France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique , Sorbonne Université, UMR 7616 CNRS , F-75005 Paris , France
- Institut Universitaire de France , F-75005 Paris , France
- The University of Texas at Austin, Department of Biomedical Engineering, Texas , United States
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27
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Célerse F, Lagardère L, Derat E, Piquemal JP. Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems. J Chem Theory Comput 2019; 15:3694-3709. [DOI: 10.1021/acs.jctc.9b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frédéric Célerse
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Physique et Théorique, FR 2622 CNRS, Sorbonne Université, 75005 Paris, France
- Laboratoire de Chimie théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Etienne Derat
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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28
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Jolly LH, Duran A, Lagardère L, Ponder JW, Ren P, Piquemal JP. Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]. ACTA ACUST UNITED AC 2019. [DOI: 10.33011/livecoms.1.2.10409] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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30
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Stamm B, Lagardère L, Polack É, Maday Y, Piquemal JP. A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms. J Chem Phys 2018; 149:124103. [PMID: 30278683 DOI: 10.1063/1.5044541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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
In this work, we provide the mathematical elements we think essential for a proper understanding of the calculus of the electrostatic energy of point-multipoles of arbitrary order under periodic boundary conditions. The emphasis is put on the expressions of the so-called self-parts of the Ewald summation where different expressions can be found in the literature. Indeed, such expressions are of prime importance in the context of new generation polarizable force field where the self-field appears in the polarization equations. We provide a general framework, where the idea of the Ewald splitting is applied to the electric potential and, subsequently, all other quantities such as the electric field, the energy, and the forces are derived consistently thereof. Mathematical well-posedness is shown for all these contributions for any order of multipolar distribution.
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Affiliation(s)
- Benjamin Stamm
- Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, Sorbonne Université, Paris, France
| | - Étienne Polack
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, Paris, France
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, LJLL, Sorbonne Université, Université Paris-Diderot SPC, CNRS, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, Paris, France
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31
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Aviat F, Lagardère L, Piquemal JP. The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces. J Chem Phys 2018; 147:161724. [PMID: 29096518 DOI: 10.1063/1.4985911] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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
In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.
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Affiliation(s)
- Félix Aviat
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Université Paris 06, UMR 7616, F-75005 Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Université Paris 06, UMR 7616, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Université Paris 06, UMR 7616, F-75005 Paris, France
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32
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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33
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Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
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Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. J Chem Theory Comput 2017; 13:4025-4033. [DOI: 10.1021/acs.jctc.7b00572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Louis Lagardère
- UPMC Univ. Paris
06, Institut des Sciences du Calcul et des Données, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jean-Philip Piquemal
- UPMC Univ. Paris
06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Institut Universitaire de France, Paris
Cedex 05, 75231, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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35
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Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J Comput Chem 2017; 38:2047-2055. [PMID: 28600826 DOI: 10.1002/jcc.24853] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/06/2017] [Indexed: 12/27/2022]
Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Matthew Harger
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
| | - Daniel Li
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Kevin Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas at Austin, Austin, Texas, 78712
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, UPMC Université Paris 06, F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France.,Institut Universitaire de France, Paris Cedex 05, 75231, France
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
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36
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Gresh N, Naseem-Khan S, Lagardère L, Piquemal JP, Sponer JE, Sponer J. Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li +, Na +, K +, and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential. J Phys Chem B 2017; 121:3997-4014. [PMID: 28363025 DOI: 10.1021/acs.jpcb.7b01836] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K+ and Na+, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the method's accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li+, Na+, K+, or Rb+) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within ΔE is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K+ or two Rb+ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France.,Institut Universitaire de France, Paris Cedex 05, 75231, France.,Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas, 78712, United States
| | - Judit E Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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37
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Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. J Chem Theory Comput 2016; 13:180-190. [PMID: 28068773 PMCID: PMC5228058 DOI: 10.1021/acs.jctc.6b00981] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
introduce a new class of methods, denoted as Truncated Conjugate
Gradient(TCG), to solve the many-body polarization energy and its
associated forces in molecular simulations (i.e. molecular dynamics
(MD) and Monte Carlo). The method consists in a fixed number of Conjugate
Gradient (CG) iterations. TCG approaches provide a scalable solution
to the polarization problem at a user-chosen cost and a corresponding
optimal accuracy. The optimality of the CG-method guarantees that
the number of the required matrix-vector products are reduced to a
minimum compared to other iterative methods. This family of methods
is non-empirical, fully adaptive, and provides analytical gradients,
avoiding therefore any energy drift in MD as compared to popular iterative
solvers. Besides speed, one great advantage of this class of approximate
methods is that their accuracy is systematically improvable. Indeed,
as the CG-method is a Krylov subspace method, the associated error
is monotonically reduced at each iteration. On top of that, two improvements
can be proposed at virtually no cost: (i) the use of preconditioners
can be employed, which leads to the Truncated Preconditioned Conjugate
Gradient (TPCG); (ii) since the residual of the final step of the
CG-method is available, one additional Picard fixed point iteration
(“peek”), equivalent to one step of Jacobi Over Relaxation
(JOR) with relaxation parameter ω, can be made at almost no
cost. This method is denoted by TCG-n(ω). Black-box adaptive
methods to find good choices of ω are provided and discussed.
Results show that TPCG-3(ω) is converged to high accuracy (a
few kcal/mol) for various types of systems including proteins and
highly charged systems at the fixed cost of four matrix-vector products:
three CG iterations plus the initial CG descent direction. Alternatively,
T(P)CG-2(ω) provides robust results at a reduced cost (three
matrix-vector products) and offers new perspectives for long polarizable
MD as a production algorithm. The T(P)CG-1(ω) level provides
less accurate solutions for inhomogeneous systems, but its applicability
to well-conditioned problems such as water is remarkable, with only
two matrix-vector product evaluations.
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Affiliation(s)
- Félix Aviat
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France
| | - Antoine Levitt
- Inria Paris, F-75589 Paris Cedex 12, Université Paris-Est, CERMICS (ENPC) , Marne-la-Vallée, F-77455, France
| | - Benjamin Stamm
- MATHCCES, Department of Mathematics, RWTH Aachen University , Schinkelstraße 2, D-52062 Aachen, Germany.,Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , Jülich, 52425, Germany
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, UPMC Université Paris 06, UMR 7598 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France.,Division of Applied Maths, Brown University , Providence, Rhode Island 02912, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis , Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut du Calcul et de la Simulation, UPMC Université Paris 06 , F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France
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38
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Loco D, Polack É, Caprasecca S, Lagardère L, Lipparini F, Piquemal JP, Mennucci B. A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations. J Chem Theory Comput 2016; 12:3654-61. [DOI: 10.1021/acs.jctc.6b00385] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
| | - Étienne Polack
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
| | - Louis Lagardère
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Sorbonne Universités,
UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Jean-Philip Piquemal
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- CNRS, UMR 7598 and 7616, F-75005, Paris, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
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39
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Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. J Chem Theory Comput 2016; 11:623-34. [PMID: 26516318 DOI: 10.1021/ct500998q] [Citation(s) in RCA: 40] [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: 01/28/2023]
Abstract
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
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Affiliation(s)
- Filippo Lipparini
- UniversitéPierre et Marie Curie−Paris 06 (UPMC), UMR 7598, Laboratoire Jacques-Louis Lions, Sorbonne Universités, F-75005, Paris, France
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40
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Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Cisneros GA. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem 2016; 37:1019-29. [PMID: 26781073 PMCID: PMC4808410 DOI: 10.1002/jcc.24295] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Abstract
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
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41
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Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J Comput Chem 2016; 37:494-506. [PMID: 26814845 PMCID: PMC4730919 DOI: 10.1002/jcc.24257] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/02/2015] [Accepted: 10/21/2015] [Indexed: 12/25/2022]
Abstract
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.
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Affiliation(s)
- Christophe Narth
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Louis Lagardère
- UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Étienne Polack
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Nohad Gresh
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Chemistry and Biology Nucleo(s)tides and immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale, Paris 75006, France
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - David R. Bell
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - Joshua A. Rackers
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Jay W. Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Pengyu Y. Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
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42
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Lipparini F, Scalmani G, Lagardère L, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy. J Chem Phys 2015; 141:184108. [PMID: 25399133 DOI: 10.1063/1.4901304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present the general theory and implementation of the Conductor-like Screening Model according to the recently developed ddCOSMO paradigm. The various quantities needed to apply ddCOSMO at different levels of theory, including quantum mechanical descriptions, are discussed in detail, with a particular focus on how to compute the integrals needed to evaluate the ddCOSMO solvation energy and its derivatives. The overall computational cost of a ddCOSMO computation is then analyzed and decomposed in the various steps: the different relative weights of such contributions are then discussed for both ddCOSMO and the fastest available alternative discretization to the COSMO equations. Finally, the scaling of the cost of the various steps with respect to the size of the solute is analyzed and discussed, showing how ddCOSMO opens significantly new possibilities when cheap or hybrid molecular mechanics/quantum mechanics methods are used to describe the solute.
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Affiliation(s)
- Filippo Lipparini
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Louis Lagardère
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Eric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
| | - Yvon Maday
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald. J Chem Theory Comput 2015; 11:2589-99. [DOI: 10.1021/acs.jctc.5b00171] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Louis Lagardère
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
| | - Filippo Lipparini
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Étienne Polack
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Benjamin Stamm
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
- CNRS, UMR 7598 and 7616, F-75005, Paris, France
| | - Éric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France
| | - Michael Schnieders
- Departments
of Biomedical Engineering and Biochemistry, The University of Iowa, Iowa City, Iowa 52358, United States
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yvon Maday
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
- Institut Universitaire de France, F-75005, Paris, France
- Division
of Applied Mathematics, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
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Caprasecca S, Jurinovich S, Lagardère L, Stamm B, Lipparini F. Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding. J Chem Theory Comput 2015; 11:694-704. [DOI: 10.1021/ct501087m] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, I-56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, I-56124 Pisa, Italy
| | - Louis Lagardère
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
- CNRS, UMR
7598
and 7616, F-75005 Paris, France
| | - Filippo Lipparini
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
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Chaudret R, Gresh N, Narth C, Lagardère L, Darden TA, Cisneros GA, Piquemal JP. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. J Phys Chem A 2014; 118:7598-612. [PMID: 24878003 DOI: 10.1021/jp5051657] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization.
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Affiliation(s)
- Robin Chaudret
- Sorbonne Universités , UPMC, Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
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Lipparini F, Lagardère L, Scalmani G, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach. J Phys Chem Lett 2014; 5:953-958. [PMID: 26270973 DOI: 10.1021/jz5002506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new implementation of continuum solvation models for semiempirical Hamiltonians that allows the description of environmental effects on very large molecular systems. In this approach based on a domain decomposition strategy of the COSMO model (ddCOSMO), the solution to the COSMO equations is no longer the computational bottleneck but becomes a negligible part of the overall computation time. In this Letter, we analyze the computational impact of COSMO on the solution of the SCF equations for large to very large molecules, using semiempirical Hamiltonians, for both the new ddCOSMO implementation and the most recent, linear scaling one, based on the fast multipole method. A further analysis is on the simulation of the UV/visible spectrum of a light-harvesting pigment-protein complex. All of the results show how the new ddCOSMO algorithm paves the way to routine computations for large molecular systems in the condensed phase.
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Affiliation(s)
- Filippo Lipparini
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, F-75005 Paris, France
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Louis Lagardère
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Giovanni Scalmani
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benjamin Stamm
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | | | - Yvon Maday
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- #Institut Universitaire de France, France
- ∇Division of Applied Maths, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | - Michael J Frisch
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benedetta Mennucci
- ◆Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. J Chem Theory Comput 2014; 10:1638-1651. [PMID: 26512230 DOI: 10.1021/ct401096t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this paper, we present a scalable and efficient implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The Smooth Particle-Mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the Direct Inversion in the Iterative Subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy-force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package which is the first implementation for a polarizable model making large scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of spme and a noticeable improvement of the memory management giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations.
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Affiliation(s)
- Louis Lagardère
- UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Filippo Lipparini
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France ; UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Étienne Polack
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Benjamin Stamm
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; CNRS, UMR 7598 and 7616, F-75005, Paris, France
| | - Éric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France
| | - Michael Schnieders
- Departments of Biomedical Engineering and Biochemistry, The University of Iowa, Iowa City, Iowa 52358, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yvon Maday
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; Institut Universitaire de France ; Brown Univ, Division of Applied Maths, Providence, RI, USA
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
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