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Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
Filippo Lipparini
,
Louis Lagardère
,
Benjamin Stamm
,
Eric Cancès
,
Michael Schnieders
,
et al.
Journal articles
hal-01090942v1
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Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs
Matthew Harger
,
Daniel Li
,
Zhi Wang
,
Kevin Dalby
,
Louis Lagardère
,
et al.
Journal articles
hal-01571313v1
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Towards scalable and accurate molecular dynamics using the SIBFA polarizable force field
Louis Lagardère
,
Léa El-Khoury
,
Sehr Naseem-Khan
,
Félix Aviat
,
Nohad Gresh
,
et al.
AIP Conference Proceedings, 2017
Journal articles
hal-01521838v1
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Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials
Thomas Plé
,
Nastasia Mauger
,
Olivier Adjoua
,
Théo Jaffrelot Inizan
,
Louis Lagardère
,
et al.
Journal articles
hal-03887583v1
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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
Rae Corrigan
,
Guowei Qi
,
Andrew Thiel
,
Jack Lynn
,
Brandon D Walker
,
et al.
Journal articles
hal-03183306v1
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Enforcing local DNA kinks by sequence-selective trisintercalating oligopeptides of a tricationic porphyrin. A polarizable Molecular Dynamics study.
Nohad Gresh
,
Krystel El Hage
,
Louis Lagardère
,
Frédérique Brégier
,
Jeremy Godard
,
et al.
2023
Preprints, Working Papers, ...
hal-04172808v1
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Force-Field-Enhanced Neural Network Interactions: from Local Equivariant Embedding to Atom-in-Molecule properties and long-range effects
Thomas Plé
,
Louis Lagardère
,
Jean-Philip Piquemal
2023
Preprints, Working Papers, ...
hal-03917901v1
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Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field
Nastasia Mauger
,
Thomas Plé
,
Louis Lagardère
,
Simon Huppert
,
Jean-Philip Piquemal
Journal articles
hal-03706599v1
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Correction to “Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Nonpolarizable Simulations of Realistic Systems”
Frédéric Célerse
,
Louis Lagardère
,
Etienne Derat
,
Jean-Philip Piquemal
Journal articles
hal-03210774v1
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Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: comparisons of polarizable and non-polarizable simulations of realistic systems
Frederic Célerse
,
Louis Lagardère
,
Etienne Derat
,
Jean-Philip Piquemal
Journal articles
hal-02122209v1
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Quantum, classical, and hybrid QM/MM calculations in solution: General implementation of the ddCOSMO linear scaling strategy
Filippo Lipparini
,
Giovanni Scalmani
,
Louis Lagardère
,
Benjamin Stamm
,
Eric Cancès
,
et al.
Journal articles
hal-01090954v1
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Filippo Lipparini
,
Louis Lagardère
,
Christophe Raynaud
,
Benjamin Stamm
,
Eric Cancès
,
et al.
Journal articles
hal-01114784v1
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The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces
Félix Aviat
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-01571663v2
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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
Nohad Gresh
,
Sehr Naseem-Khan
,
Louis Lagardère
,
Jean-Philip Piquemal
,
Judit E. Sponer
,
et al.
Journal articles
hal-01502376v1
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How to make continuum solvation incredibly fast in a few simple steps: a practical guide to the domain decomposition paradigm for the Conductor-like Screening Model Continuum Solvation, Linear Scaling, Domain Decomposition
Benjamin Stamm
,
Louis Lagardère
,
Giovanni Scalmani
,
Paolo Gatto
,
Eric Cancès
,
et al.
Journal articles
hal-01793770v1
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Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm
Pier P. Poier
,
Louis Lagardère
,
Jean-Philip Piquemal
2023
Preprints, Working Papers, ...
hal-04153125v1
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A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations
Daniele Loco
,
Etienne Polack
,
Stefano Caprasecca
,
Louis Lagardère
,
Filippo Lipparini
,
et al.
Journal articles
hal-02126716v1
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Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including Long-range Effects
Théo Jaffrelot-Inizan
,
Thomas Plé
,
Olivier Adjoua
,
Pengyu Ren
,
Hatice Gökcan
,
et al.
Journal articles
hal-03738403v1
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Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations
Louis Lagardère
,
Lise Maurin
,
Olivier Adjoua
,
Krystel EL Hage
,
Pierre Monmarché
,
et al.
2023
Preprints, Working Papers, ...
hal-04162777v1
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QM / AMOEBA description of properties and dynamics of embedded molecules
Michele Nottoli
,
Mattia Bondanza
,
Patrizia Mazzeo
,
Lorenzo Cupellini
,
Carles Curutchet
,
et al.
Journal articles
hal-04122813v1
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ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations
Igor Chollet
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-03902427v1
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Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach
Filippo Lipparini
,
Louis Lagardère
,
Giovanni Scalmani
,
Benjamin Stamm
,
Eric Cancès
,
et al.
Journal articles
hal-00956401v1
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Computationally driven discovery of targeting SARS-CoV-2 Mpro inhibitors: from design to experimental validation
Léa El Khoury
,
Zhifeng Jing
,
Daniele Loco
,
Alberto Cuzzolin
,
Alessandro Deplano
,
et al.
Journal articles
hal-03361062v1
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Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory
Pier Paolo Poier
,
Olivier Adjoua
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-03819436v1
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Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface
Dina El Ahdab
,
Louis Lagardère
,
Theo Jaffrelot Inizan
,
Frédéric Célerse
,
Chengwen Liu
,
et al.
Journal articles
hal-03220156v1
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Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory
Pier Paolo Poier
,
Théo Jaffrelot Inizan
,
Olivier Adjoua
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-03624156v1
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Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators
Krystel El Hage
,
Giovanni Ribaudo
,
Louis Lagardère
,
Alberto Ongaro
,
Philippe H. Kahn
,
et al.
Journal articles
hal-03624169v1
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β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions
Adrien Schahl
,
Louis Lagardère
,
Brandon Walker
,
Pengyu Ren
,
Antoine Jégoud
,
et al.
2022
Preprints, Working Papers, ...
hal-03904639v1
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Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations
Léa El-Khoury
,
Frederic Célerse
,
Louis Lagardère
,
Luc-Henri Jolly
,
Etienne Derat
,
et al.
Journal articles
hal-03046841v1
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Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics
Louis Lagardère
,
Félix Aviat
,
Jean-Philip Piquemal
Journal articles
hal-02119888v1
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