Molecular latent space simulators
Abstract
Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing configurational or dynamical coarse-graining of the state space. The learned kinetic models enable the efficient generation of dynamical trajectories over vastly longer time scales than are accessible by MD, but the discretization of configurational space and/or absence of a means to reconstruct molecular configurations precludes the generation of continuous all-atom molecular trajectories. We propose latent space simulators (LSS) to learn kinetic models for continuous all-atom simulation trajectories by training three deep learning networks to (i) learn the slow collective variables of the molecular system, (ii) propagate the system dynamics within this slow latent space, and (iii) generatively reconstruct molecular configurations. We demonstrate the approach in an application to Trp-cage miniprotein to produce novel ultra-long synthetic folding trajectories that accurately reproduce all-atom molecular structure, thermodynamics, and kinetics at six orders of magnitude lower cost than MD. The dramatically lower cost of trajectory generation enables greatly improved sampling and greatly reduced statistical uncertainties in estimated thermodynamic averages and kinetic rates.
- Authors:
-
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division
- OSTI Identifier:
- 1657300
- Alternate Identifier(s):
- OSTI ID: 1651122
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- Chemical Science
- Additional Journal Information:
- Journal Name: Chemical Science Journal Volume: 11 Journal Issue: 35; Journal ID: ISSN 2041-6520
- Publisher:
- Royal Society of Chemistry
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
Sidky, Hythem, Chen, Wei, and Ferguson, Andrew L. Molecular latent space simulators. United Kingdom: N. p., 2020.
Web. doi:10.1039/D0SC03635H.
Sidky, Hythem, Chen, Wei, & Ferguson, Andrew L. Molecular latent space simulators. United Kingdom. https://doi.org/10.1039/D0SC03635H
Sidky, Hythem, Chen, Wei, and Ferguson, Andrew L. Wed .
"Molecular latent space simulators". United Kingdom. https://doi.org/10.1039/D0SC03635H.
@article{osti_1657300,
title = {Molecular latent space simulators},
author = {Sidky, Hythem and Chen, Wei and Ferguson, Andrew L.},
abstractNote = {Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing configurational or dynamical coarse-graining of the state space. The learned kinetic models enable the efficient generation of dynamical trajectories over vastly longer time scales than are accessible by MD, but the discretization of configurational space and/or absence of a means to reconstruct molecular configurations precludes the generation of continuous all-atom molecular trajectories. We propose latent space simulators (LSS) to learn kinetic models for continuous all-atom simulation trajectories by training three deep learning networks to (i) learn the slow collective variables of the molecular system, (ii) propagate the system dynamics within this slow latent space, and (iii) generatively reconstruct molecular configurations. We demonstrate the approach in an application to Trp-cage miniprotein to produce novel ultra-long synthetic folding trajectories that accurately reproduce all-atom molecular structure, thermodynamics, and kinetics at six orders of magnitude lower cost than MD. The dramatically lower cost of trajectory generation enables greatly improved sampling and greatly reduced statistical uncertainties in estimated thermodynamic averages and kinetic rates.},
doi = {10.1039/D0SC03635H},
journal = {Chemical Science},
number = 35,
volume = 11,
place = {United Kingdom},
year = {Wed Sep 16 00:00:00 EDT 2020},
month = {Wed Sep 16 00:00:00 EDT 2020}
}
https://doi.org/10.1039/D0SC03635H
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