ArticleJournal of chemical theory and computation2010
Automated sampling assessment for molecular simulations using the effective sample size.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed.
- Molecular and Biological Investigation of Isolated Marine Fungal Metabolites as Anticancer Agents: A Multi-Target Approach.Metabolites · 2023Article
- Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.Journal of chemical theory and computation · 2022Article
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.Journal of chemical information and modeling · 2019Article
- Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].Living journal of computational molecular science · 2018Article
- Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.Journal of chemical theory and computation · 2014Article
- Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Journal of chemical theory and computation · 2014Article
- Finding semirigid domains in biomolecules by clustering pair-distance variations.BioMed research international · 2014Article
- Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure.BMC structural biology · 2013Article
- Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.Journal of chemical theory and computation · 2012Article
- Relaxation estimation of RMSD in molecular dynamics immunosimulations.Computational and mathematical methods in medicine · 2012Article
- Equilibrium sampling in biomolecular simulations.Annual review of biophysics · 2011Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
To quantify the progress in the development of algorithms and forcefields used in molecular simulations, a general method for the assessment of the sampling quality is needed. Statistical mechanics principles suggest the populations of physical states characterize equilibrium sampling in a fundamental way. We therefore develop an approach for analyzing the variances in state populations, which quantifies the degree of sampling in terms of the effective sample size (ESS). The ESS estimates the number of statistically independent configurations contained in a simulated ensemble. The method is applicable to both traditional dynamics simulations as well as more modern (e.g., multi-canonical) approaches. Our procedure is tested in a variety of systems from toy models to atomistic protein simulations. We also introduce a simple automated procedure to obtain approximate physical states from dynamic trajectories: this allows sample-size estimation in systems for which physical states are not known in advance.
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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.