ArticleJournal of chemical information and modeling2014
AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRASJournal of chemical information and modeling · 2024Article
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis.Journal of chemical information and modeling · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.Briefings in bioinformatics · 2021Review
- Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.ACS omega · 2020Article
- Enhanced Jarzynski free energy calculations using weighted ensemble.The Journal of chemical physics · 2020Article
- Why Awe Promotes Prosocial Behaviors? The Mediating Effects of Future Time Perspective and Self-Transcendence Meaning of Life.Frontiers in psychology · 2019Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.Protein science : a publication of the Protein Society · 2016Article
- A comparison of weighted ensemble and Markov state model methodologies.The Journal of chemical physics · 2015Article
- WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis.Journal of chemical theory and computation · 2015Article
- Molecular dynamics simulations: advances and applications.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- 15 Years of molecular simulation of drug-binding kinetics.Expert opinion on drug discoveryReview
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
7 authors.
Funding
Abstract
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 high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and allow calculation of unbiased rates. However, while WE can sample correctly and efficiently, a scalable implementation applicable to interesting biomolecular systems is not available. We provide here a GPLv2 implementation called AWE-WQ of a WE algorithm using the master/worker distributed computing WorkQueue (WQ) framework. AWE-WQ is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage (such as central processing units (CPU) and graphical processing units (GPUs) concurrently), seamless heterogeneous cluster usage (i.e., campus grids and cloud providers), and support for arbitrary MD codes such as GROMACS, while ensuring that all statistics are unbiased. We applied AWE-WQ to a 34 residue protein which simulated 1.5 ms over 8 months with peak aggregate performance of 1000 ns/h. Comparison was done with a 200 μs simulation collected on a GPU over a similar timespan. The folding and unfolded rates were of comparable accuracy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.