ArticleThe journal of physical chemistry. B2013
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- 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
- 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
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.Journal of chemical theory and computation · 2020Article
- Computational methods for exploring protein conformations.Biochemical Society transactions · 2020Review
- A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions.Communications in information and systems · 2020Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
- Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.PLoS computational biology · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- RNA force field with accuracy comparable to state-of-the-art protein force fields.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].Living journal of computational molecular science · 2018Article
- Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.Journal of chemical theory and computation · 2017Article
- Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.Journal of chemical theory and computation · 2016Article
- Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.Journal of chemical theory and computation · 2016Article
- Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.Journal of chemical theory and computation · 2016Article
- Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 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
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3 authors.
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Abstract
Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.
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