Louis Lagardère

发表

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems.

J. Piquemal, Frédéric Célerse, Louis Lagardère, 2019, Journal of chemical theory and computation.

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

Nohad Gresh, Jean-Philip Piquemal, Jay W. Ponder, 2015, Journal of chemical theory and computation.

Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics.

Jean-Philip Piquemal, Louis Lagardère, Félix Aviat, 2019, The journal of physical chemistry letters.

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. Šponer, J. Šponer, J. Šponer, 2017, The journal of physical chemistry. B.

A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms.

Y. Maday, J. Piquemal, B. Stamm, 2018, The Journal of chemical physics.

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]

Jean-Philip Piquemal, Alejandro Duran, Jay W. Ponder, 2019, Living Journal of Computational Molecular Science.

Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics

Krystel El Hage, F. Lipparini, D. Pérahia, 2015 .

A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations.

Jean-Philip Piquemal, Benedetta Mennucci, Louis Lagardère, 2016, Journal of chemical theory and computation.

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

F. Lipparini, M. Frisch, J. Piquemal, 2019, Chemical science.

Towards scalable and accurate molecular dynamics using the SIBFA polarizable force field

N. Gresh, J. Piquemal, Louis Lagardère, 2017 .

Molecular Dynamics with AMOEBA Polarizable Embedding

F. Lipparini, J. Piquemal, S. Caprasecca, 2017 .

Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach.

Benjamin Stamm, Giovanni Scalmani, Yvon Maday, 2014, The journal of physical chemistry letters.

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.

Nohad Gresh, Jean-Philip Piquemal, Louis Lagardère, 2014, The journal of physical chemistry. A.

AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

Jean-Philip Piquemal, Louis Lagardère, J. Piquemal, 2018, Journal of chemical theory and computation.

An Efficient GaMD Multi-Level Enhanced Sampling Strategy for Polarizable Force Fields Simulations of Large Biological Systems

Jean-Philip Piquemal, Louis Lagardère, Olivier Adjoua, 2021 .

High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Pengyu Y. Ren, M. Montès, Cheng-Wen Liu, 2020 .

Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

J. Piquemal, S. Huppert, Louis Lagardère, 2022, 2206.13430.

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.

Brandon D. Walker, Pengyu Y. Ren, J. Ponder, 2020, Journal of chemical theory and computation.

Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model.

F. Jensen, J. Piquemal, Louis Lagardère, 2019, Journal of chemical theory and computation.

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations.

Pengyu Y. Ren, N. Gresh, J. Piquemal, 2019, Journal of chemical theory and computation.

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations.

Pengyu Y. Ren, N. Gresh, J. Piquemal, 2022, Journal of chemical theory and computation.

Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

J. Piquemal, S. Huppert, Louis Lagardère, 2022, 2206.13430.

Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field.

J. Piquemal, Thomas Plé, S. Huppert, 2022, The journal of physical chemistry. B.

Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected DFT Non-Covalent

Th'eo Jaffrelot Inizan, J. Piquemal, Louis Lagardère, 2022 .

Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory.

J. Piquemal, Louis Lagardère, Pier Paolo Poier, 2022, The journal of physical chemistry letters.

Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects

Th'eo Jaffrelot Inizan, Pengyu Y. Ren, O. Isayev, 2022, Chemical science.

Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory

J. Piquemal, Louis Lagardère, Pier Paolo Poier, 2022, ArXiv.

Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: From Force Fields to Machine Learning Potentials.

J. Piquemal, S. Huppert, Louis Lagardère, 2022, Journal of chemical theory and computation.

ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations

J. Piquemal, Louis Lagardère, I. Chollet, 2022, Journal of chemical theory and computation.

β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions

Brandon D. Walker, Pengyu Y. Ren, M. Chavent, 2022, bioRxiv.

Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath.

J. Piquemal, Thomas Plé, S. Huppert, 2021, The journal of physical chemistry letters.

Generalized Many-Body Dispersion Correction through Random-Phase Approximation for Chemically Accurate Density Functional Theory

J. Piquemal, Louis Lagardère, Pier Paolo Poier, 2022, The journal of physical chemistry letters.

O(N)Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

J. Piquemal, Louis Lagardère, Pier Paolo Poier, 2021 .

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems.

J. Piquemal, Louis Lagardère, Pier Paolo Poier, 2022, Journal of chemical theory and computation.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

Nohad Gresh, Benjamin Stamm, Yvon Maday, 2017, Chemical science.

Tinker 8: Software Tools for Molecular Design.

Jean-Philip Piquemal, Zhi Wang, Louis Lagardère, 2018, Journal of chemical theory and computation.

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

Krystel El Hage, N. Gresh, J. Piquemal, 2022, J. Chem. Inf. Model..

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

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2018, International Journal of Quantum Chemistry.

Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface

Pengyu Y. Ren, N. Gresh, J. Piquemal, 2021, The journal of physical chemistry letters.

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0] pdf

Jean-Philip Piquemal, Alejandro Duran, Louis Lagardère, 2019, ArXiv.

Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Zhi Wang, Jean-Philip Piquemal, Kevin N. Dalby, 2017, J. Comput. Chem..

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles

Nohad Gresh, Jean-Philip Piquemal, Qiantao Wang, 2016, J. Comput. Chem..

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

Benjamin Stamm, Yvon Maday, Pengyu Ren, 2015, Journal of chemical theory and computation.

Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy.

Benjamin Stamm, Giovanni Scalmani, Yvon Maday, 2014, The Journal of chemical physics.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2014 .

Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.

Jean-Philip Piquemal, Benedetta Mennucci, Louis Lagardère, 2017, Journal of chemical theory and computation.

Achieving linear scaling in computational cost for a fully polarizable MM/continuum embedding.

Benjamin Stamm, Louis Lagardère, Sandro Jurinovich, 2015, Journal of chemical theory and computation.

Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation

Pengyu Y. Ren, J. Ponder, M. Sturlese, 2021, Chemical science.

Force-Field-Enhanced Neural Network Interactions: from Local Equivariant Embedding to Atom-in-Molecule properties and long-range effects

J. Piquemal, Louis Lagardère, Thomas Pl'e, 2023, 2301.08734.

Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity

J. Piquemal, Louis Lagardère, Daniele Loco, 2021, Accounts of chemical research.

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations.

Pengyu Y. Ren, N. Gresh, J. Piquemal, 2022, Journal of chemical theory and computation.

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Pengyu Y. Ren, J. Ponder, J. Piquemal, 2021, Journal of chemical theory and computation.

Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems

Jean-Philip Piquemal, Zhi Wang, Jay W. Ponder, 2020, ArXiv.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces.

Jean-Philip Piquemal, Louis Lagardère, Félix Aviat, 2017, The Journal of chemical physics.

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2016, Journal of chemical theory and computation.

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields

Jean-Philip Piquemal, Louis Lagardère, Alice R. Walker, 2016, J. Comput. Chem..

Polarizable molecular dynamics in a polarizable continuum solvent.

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2015, Journal of chemical theory and computation.

Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm

J. Piquemal, Louis Lagardère, P. P. Poier, 2023, 2307.02278.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Pengyu Y. Ren, J. Ponder, F. Lipparini, 2017, Chemical science.

Tinker 8: Software Tools for Molecular Design.

Marie L. Laury, Joshua A. Rackers, Pengyu Y. Ren, 2018, Journal of chemical theory and computation.

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

F. Lipparini, M. Frisch, G. Cisneros, 2019, Chemical science.

Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects

Louis Lagardère, Thomas Pl'e, Jean‐Philip Piquemal, 2023, Chemical science.

Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Pengyu Y. Ren, J. Ponder, Matthew Harger, 2017, J. Comput. Chem..

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.

Pierre Monmarché, Frédéric Célerse, Louis Lagardère, 2022, Journal of chemical theory and computation.

Enforcing local DNA kinks by sequence-selective trisintercalating oligopeptides of a tricationic porphyrin. A polarizable Molecular Dynamics study

Krystel El Hage, N. Gresh, V. Sol, 2023, bioRxiv.

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems.

Louis Lagardère, P. P. Poier, Jean‐Philip Piquemal, 2021, Journal of chemical theory and computation.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems.

Frédéric Célerse, Louis Lagardère, E. Derat, 2019, Journal of chemical theory and computation.

QM/AMOEBA description of properties and dynamics of embedded molecules

F. Lipparini, C. Curutchet, B. Mennucci, 2022 .

Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations.

Pierre Monmarché, Louis Lagardère, Jean‐Philip Piquemal, 2020, The Journal of chemical physics.

Unveiling the Full Dynamical and Reactivity Profiles of Acetylcholinesterase: A Comprehensive All-Atom Investigation

Frédéric Célerse, Louis Lagardère, F. Nachon, 2024, ACS Catalysis.

Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics.

Louis Lagardère, Félix Aviat, Jean‐Philip Piquemal, 2019, The journal of physical chemistry letters.

Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory.

Louis Lagardère, Olivier Adjoua, Théo Jaffrelot Inizan, 2022, The journal of physical chemistry letters.

Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors

Brandon D. Walker, Pengyu Y. Ren, M. Chavent, 2024, bioRxiv.

FeNNol: an Efficient and Flexible Library for Building Force-field-enhanced Neural Network Potentials

Louis Lagardère, Olivier Adjoua, Jean‐Philip Piquemal, 2024, The Journal of chemical physics.