DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling
Recent advances in computational power and algorithms have enabled molecular dynamics
(MD) simulations to reach greater time scales. However, for observing conformational …
(MD) simulations to reach greater time scales. However, for observing conformational …
Accelerated estimation of long-timescale kinetics from weighted ensemble simulation via non-Markovian “microbin” analysis
J Copperman, DM Zuckerman - Journal of chemical theory and …, 2020 - ACS Publications
The weighted ensemble (WE) simulation strategy provides unbiased sampling of
nonequilibrium processes, such as molecular folding or binding, but the extraction of rate …
nonequilibrium processes, such as molecular folding or binding, but the extraction of rate …
Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
Interest in atomically detailed simulations has grown significantly with recent advances in
computational hardware and Markov state modeling (MSM) methods, yet outstanding …
computational hardware and Markov state modeling (MSM) methods, yet outstanding …
AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble
B Abdul-Wahid, H Feng, D Rajan… - Journal of chemical …, 2014 - ACS Publications
A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to
compute. This is due to the rarity of observing transitions between metastable states since …
compute. This is due to the rarity of observing transitions between metastable states since …
[HTML][HTML] Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm
Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic
properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not …
properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not …
Accelerated simulations of molecular systems through learning of effective dynamics
Simulations are vital for understanding and predicting the evolution of complex molecular
systems. However, despite advances in algorithms and special purpose hardware …
systems. However, despite advances in algorithms and special purpose hardware …
WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications
The weighted ensemble (WE) family of methods is one of several statistical mechanics-
based path sampling strategies that can provide estimates of key observables (rate …
based path sampling strategies that can provide estimates of key observables (rate …
Gaussian-accelerated molecular dynamics with the weighted ensemble method: A hybrid method improves thermodynamic and kinetic sampling
Gaussian-accelerated molecular dynamics (GaMD) is a well-established enhanced
sampling method for molecular dynamics simulations that effectively samples the potential …
sampling method for molecular dynamics simulations that effectively samples the potential …
Adaptive sampling methods for molecular dynamics in the era of machine learning
Molecular dynamics (MD) simulations are fundamental computational tools for the study of
proteins and their free energy landscapes. However, sampling protein conformational …
proteins and their free energy landscapes. However, sampling protein conformational …
Unbiasing Enhanced Sampling on a High-Dimensional Free Energy Surface with a Deep Generative Model
Biased enhanced sampling methods that utilize collective variables (CVs) are powerful tools
for sampling conformational ensembles. Due to their large intrinsic dimensions, efficiently …
for sampling conformational ensembles. Due to their large intrinsic dimensions, efficiently …