arXiv subjects

Louis Lagardère

Publications and source records attributed to Louis Lagardère.

27 records · Page 2Linked to original sources

arXiv2022

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

We present the extension of the SIBFA (Sum of Interactions Between Fragments Ab initio Computed 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.

physics.chem-ph↗

arXiv2022

Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory

Using a Deep Neuronal Network model (DNN) trained on the large ANI-1 data set of small organic molecules, we propose a transferable density-free many-body dispersion model (DNN-MBD). 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 MBD's applicability beyond electronic structure theory within methodologies such as force fields and neural networks.

physics.chem-ph↗

arXiv2022

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

GC-rich sequences are recurring motifs in oncogenes and retroviruses, and could be targeted by non-covalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anti-cancer intercalator mitoxantrone. The stability of their complexes with a 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 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 an even higher selectivity, targeting an increased number of DNA bases, going beyond ten.

physics.chem-ph↗

arXiv2021

Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath

We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQE) 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 we 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 classical molecular dynamics, enabling simulations of up to millions of degrees of freedom.

physics.chem-ph↗

arXiv2021

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

This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in Tinker-HP and dedicated to perform large scale simulations. We show how it can be adapted to recent Intel Central Processing Unit (CPU) petascale architectures. First, we discuss the new set of Intel Advanced Vector Extensions 512 (Intel AVX-512) instructions present in recent Intel processors (e.g., the Intel Xeon Scalable and Intel Xeon Phi 2nd generation processors) allowing for larger vectorization enhancements. These instructions constitute the central source of potential computational gains when using the latest processors, justifying important vectorization efforts for developers. We then briefly review the organization of the Tinker-HP code and identify the computational hotspots which require Intel AVX-512 optimization and we propose a general and optimal strategy to vectorize those particular parts of the code. We intended to present our optimization strategy in a pedagogical way so it could benefit to other researchers and students interested in gaining performances in their own software. Finally we present the performance enhancements obtained compared to the unoptimized code both sequentially and at the scaling limit in parallel for classical non-polarizable (CHARMM) and polarizable force fields (AMOEBA). This paper never ceases to be updated as we accumulate new data on the associated Github repository between new versions of this living paper.

cs.MS↗

arXiv2021

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

We present the extension of the Tinker-HP package (Lagardère 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).

physics.comp-ph↗

arXiv2020

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

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 (2-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 is tested in the cases of pure direct-space droplet-like simulations and of periodic boundary conditions (PBC) simulations using Smooth Particule Mesh Ewald. An analysis of the capability of BOUNCE to reproduce several condensed phase properties is provided. Since electrostatics and van der Waals 2-body contributions are evaluated much less often than with standard integrators using a 1fs timestep, 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 integrator by the BOUNCE adaptive framework preserves a similar accuracy and leads to significant computational savings.

physics.chem-ph↗

arXiv2018

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

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 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.

physics.chem-ph↗

arXiv2017

The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces

In a recent paper (J. Chem. Theory. Comput., 2017, 13, 180-190) 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 1

physics.chem-ph↗