Literature DB >> 31050904

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

Louis Lagardère1,2, Félix Aviat2,3, Jean-Philip Piquemal3,4,5.   

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.

Entities:  

Year:  2019        PMID: 31050904     DOI: 10.1021/acs.jpclett.9b00901

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  7 in total

1.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

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

Authors:  Olivier Adjoua; Louis Lagardère; Luc-Henri Jolly; Arnaud Durocher; Thibaut Very; Isabelle Dupays; Zhi Wang; Théo Jaffrelot Inizan; Frédéric Célerse; Pengyu Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2021-03-23       Impact factor: 6.006

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

Authors:  Léa El Khoury; Zhifeng Jing; Alberto Cuzzolin; Alessandro Deplano; Daniele Loco; Boris Sattarov; Florent Hédin; Sebastian Wendeborn; Chris Ho; Dina El Ahdab; Theo Jaffrelot Inizan; Mattia Sturlese; Alice Sosic; Martina Volpiana; Angela Lugato; Marco Barone; Barbara Gatto; Maria Ludovica Macchia; Massimo Bellanda; Roberto Battistutta; Cristiano Salata; Ivan Kondratov; Rustam Iminov; Andrii Khairulin; Yaroslav Mykhalonok; Anton Pochepko; Volodymyr Chashka-Ratushnyi; Iaroslava Kos; Stefano Moro; Matthieu Montes; Pengyu Ren; Jay W Ponder; Louis Lagardère; Jean-Philip Piquemal; Davide Sabbadin
Journal:  Chem Sci       Date:  2022-02-10       Impact factor: 9.825

4.  High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling.

Authors:  Théo Jaffrelot Inizan; Frédéric Célerse; Olivier Adjoua; Dina El Ahdab; Luc-Henri Jolly; Chengwen Liu; Pengyu Ren; Matthieu Montes; Nathalie Lagarde; Louis Lagardère; Pierre Monmarché; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2021-02-02       Impact factor: 9.825

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

Authors:  Daniele Loco; Louis Lagardère; Gérardo A Cisneros; Giovanni Scalmani; Michael Frisch; Filippo Lipparini; Benedetta Mennucci; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2019-06-11       Impact factor: 9.825

6.  Accurate Biomolecular Simulations Account for Electronic Polarization.

Authors:  Josef Melcr; Jean-Philip Piquemal
Journal:  Front Mol Biosci       Date:  2019-12-04

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

Authors:  Dina El Ahdab; Louis Lagardère; Théo Jaffrelot Inizan; Fréderic Célerse; Chengwen Liu; Olivier Adjoua; Luc-Henri Jolly; Nohad Gresh; Zeina Hobaika; Pengyu Ren; Richard G Maroun; Jean-Philip Piquemal
Journal:  J Phys Chem Lett       Date:  2021-07-01       Impact factor: 6.475

  7 in total

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