An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems
| Autor: | Frédéric Célerse, Théo Jaffrelot Inizan, Louis Lagardère, Olivier Adjoua, Pierre Monmarché, Yinglong Miao, Etienne Derat, Jean-Philip Piquemal |
|---|---|
| Přispěvatelé: | Laboratoire de chimie théorique (LCT), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Parisien de Chimie Moléculaire (IPCM), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Kansas [Kansas City], Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), European Project: 810367,EMC2(2019) |
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Water
gaussian accelerated molecular dynamics Molecular Dynamics Simulation Molecular dynamics umbrella sampling Adaptive sampling enhanced sampling Computer Science Applications [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry AMOEBA polarizable force field polarizable force field Solvents Thermodynamics Potential of mean force Physical and Theoretical Chemistry |
| Zdroj: | Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation, 2022, 18 (2), pp.968-977. ⟨10.1021/acs.jctc.1c01024⟩ |
| ISSN: | 1549-9618 1549-9626 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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