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Issue 35, 2020
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Molecular latent space simulators

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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 atomistic molecular trajectories. We propose latent space simulators (LSS) to learn kinetic models for continuous atomistic 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 atomistic 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.

Graphical abstract: Molecular latent space simulators

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Article information


Submitted
01 Jul 2020
Accepted
20 Aug 2020
First published
26 Aug 2020

This article is Open Access
All publication charges for this article have been paid for by the Royal Society of Chemistry

Chem. Sci., 2020,11, 9459-9467
Article type
Edge Article

Molecular latent space simulators

H. Sidky, W. Chen and A. L. Ferguson, Chem. Sci., 2020, 11, 9459
DOI: 10.1039/D0SC03635H

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    [Original citation] - Published by The Royal Society of Chemistry.

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