ArticleJournal of chemical theory and computation2014
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular biology · 2026Review
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- 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
- Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability.Journal of chemical theory and computation · 2024Article
- Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Three-dimensional quantitative structural-activity relationship and molecular dynamics study of multivariate substituted 4-oxyquinazoline HDAC6 inhibitors.Molecular diversity · 2023Article
- Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent.Journal of chemical theory and computation · 2023Article
- Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.Journal of chemical information and modeling · 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
- Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.RNA (New York, N.Y.) · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex.PLoS computational biology · 2022Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection.Frontiers in molecular biosciences · 2021Article
- Molecular Dynamics Simulation Techniques as Tools in Drug Discovery and Pharmacology: A Focus on Allosteric Drugs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step.Communications biology · 2020Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
A necessary step to properly assess and validate the performance of force fields for biomolecules is to exhaustively sample the accessible conformational space, which is challenging for large RNA structures. Given questions regarding the reliability of modeling RNA structure and dynamics with current methods, we have begun to use RNA tetranucleotides to evaluate force fields. These systems, though small, display considerable conformational variability and complete sampling with standard simulation methods remains challenging. Here we compare and discuss the performance of known variations of replica exchange molecular dynamics (REMD) methods, specifically temperature REMD (T-REMD), Hamiltonian REMD (H-REMD), and multidimensional REMD (M-REMD) methods, which have been implemented in Amber's accelerated GPU code. Using two independent simulations, we show that M-REMD not only makes very efficient use of emerging large-scale GPU clusters, like Blue Waters at the University of Illinois, but also is critically important in generating the converged ensemble more efficiently than either T-REMD or H-REMD. With 57.6 μs aggregate sampling of a conformational ensemble with M-REMD methods, the populations can be compared to NMR data to evaluate force field reliability and further understand how putative changes to the force field may alter populations to be in more consistent agreement with experiment.
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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.