Deep learning the slow modes for rare events sampling

The role of water in host-guest interaction

(2021) Valerio Rizzi et al.   Nature Communications

Collective variables for the study of crystallisation

(2021) Tarak Karmakar et al.   MOLECULAR PHYSICS

Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling

(2021) Jakub Rydzewski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations

(2021) Sun-Ting Tsai et al.   Journal of Chemical Theory and Computation

Deep learning the slow modes for rare events sampling

(2021) Luigi Bonati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Data-Driven Collective Variables for Enhanced Sampling

(2020) Luigi Bonati et al.   Journal of Physical Chemistry Letters

Rethinking Metadynamics: From Bias Potentials to Probability Distributions

(2020) Michele Invernizzi et al.   Journal of Physical Chemistry Letters

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

(2020) Hythem Sidky et al.   MOLECULAR PHYSICS

Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics

(2020) Jayashrita Debnath et al.   Journal of Physical Chemistry Letters

Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation

(2019) Michele Invernizzi et al.   Journal of Chemical Theory and Computation

Improving collective variables: The case of crystallization

(2019) Yue-Yu Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Calculation of phase diagrams in the multithermal-multibaric ensemble

(2019) Pablo M. Piaggi et al.   JOURNAL OF CHEMICAL PHYSICS

Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets

(2019) Wei Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

Neural networks-based variationally enhanced sampling

(2019) Luigi Bonati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics

(2019) Yihang Wang et al.   Nature Communications

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer et al.   JOURNAL OF CHEMICAL PHYSICS

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling

(2018) Yi Isaac Yang et al.   Journal of Chemical Theory and Computation

Analysis of Structural Stability of Chignolin

(2018) Yutaka Maruyama et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Machine Learning of Biomolecular Reaction Coordinates

(2018) Simon Brandt et al.   Journal of Physical Chemistry Letters

Collective Variables from Local Fluctuations

(2018) Dan Mendels et al.   Journal of Physical Chemistry Letters

Unfolding Hidden Barriers by Active Enhanced Sampling

(2018) Jing Zhang et al.   PHYSICAL REVIEW LETTERS

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Automated design of collective variables using supervised machine learning

(2018) Mohammad M. Sultan et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics with Discriminants: A Tool for Understanding Chemistry

(2018) GiovanniMaria Piccini et al.   Journal of Chemical Theory and Computation

Folding a small protein using harmonic linear discriminant analysis

(2018) Dan Mendels et al.   JOURNAL OF CHEMICAL PHYSICS

Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks

(2018) Ruben Demuynck et al.   Journal of Chemical Theory and Computation

Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics

(2018) Luigi Bonati et al.   PHYSICAL REVIEW LETTERS

A variational conformational dynamics approach to the selection of collective variables in metadynamics

(2017) James McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

(2017) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling the mechanism of CLN025 beta-hairpin formation

(2017) Keri A. McKiernan et al.   JOURNAL OF CHEMICAL PHYSICS

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

(2017) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

(2016) Patrick Shaffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method

(2013) Hisashi Okumura   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

(2012) Petra Kührová et al.   BIOPHYSICAL JOURNAL

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

(2009) Alexander Stukowski   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS