ArticleThe journal of physical chemistry. B2007
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.
Article in The journal of physical chemistry. B, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Conformational dynamics underlying atypical chemokine receptor 3 activation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.Journal of chemical theory and computation · 2023Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.Journal of chemical theory and computation · 2020Article
- Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?Frontiers in molecular biosciences · 2020Review
- 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
- Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019Article
- Protein structure predictions by enhanced conformational sampling methods.Biophysics and physicobiology · 2019Review
- Reservoir pH replica exchange.The Journal of chemical physics · 2018Article
- Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Journal of molecular recognition : JMR · 2016Article
- Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.Proteins · 2015Article
- TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent.The Journal of chemical physics · 2015Article
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.Journal of computational chemistry · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling by using high temperatures to escape kinetic traps. Several groups, including ours, introduced the idea of coupling replica exchange to a pre-converged, Boltzmann-populated reservoir, usually at a temperature higher than that of the highest temperature replica. This procedure reduces computational cost because the long simulation times needed for extensive sampling are only carried out for a single temperature. However, a weakness of the approach is that the Boltzmann-weighted reservoir can still be difficult to generate. We now present the idea of employing a non-Boltzmann reservoir, whose structures can be generated through more efficient conformational sampling methods. We demonstrate that the approach is rigorous and derive a correct statistical mechanical exchange criterion between the reservoir and the replicas that drives Boltzmann-weighted probabilities for the replicas. We test this approach on the trpzip2 peptide and demonstrate that the resulting thermal stability profile is essentially indistinguishable from that obtained using very long (>100 ns) standard REMD simulations. The convergence of this reservoir-aided REMD is significantly faster than for regular REMD. Furthermore, we demonstrate that modification of the exchange criterion is essential; REMD simulations using a standard exchange function with the non-Boltzmann reservoir produced incorrect results.
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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.