ArticleThe Journal of chemical physics2011
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.Journal of chemical theory and computation · 2019Article
- VAMPnets for deep learning of molecular kinetics.Nature communications · 2018Article
- Computational membrane biophysics: From ion channel interactions with drugs to cellular function.Biochimica et biophysica acta. Proteins and proteomics · 2017Review
- Multiensemble Markov models of molecular thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A comparison of weighted ensemble and Markov state model methodologies.The Journal of chemical physics · 2015Article
- Pathways for virus assembly around nucleic acids.Journal of molecular biology · 2014Article
- On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.Journal of chemical theory and computation · 2014Article
- Using Markov state models to study self-assembly.The Journal of chemical physics · 2014Article
- Markov state models of biomolecular conformational dynamics.Current opinion in structural biology · 2014Review
- Microsecond folding experiments and simulations: a match is made.Physical chemistry chemical physics : PCCP · 2013Article
- A derivation of the master equation from path entropy maximization.The Journal of chemical physics · 2012Article
- Article
- Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.The Journal of chemical physics · 2011Article
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6 authors.
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Abstract
Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.
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