ArticleBiochimica et biophysica acta2015
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).
Article in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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75 citing papers in PubMed.
- Predicting an intrinsic conformational twist in Card1: an in silico study.Journal of molecular modeling · 2026Article
- Synthesis, Biological Activity, and Molecular Dynamics Simulations of LNA-Charge Neutral Linkages for Enhanced Splice-Switching Antisense Oligonucleotides.Angewandte Chemie (International ed. in English) · 2025Article
- Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles.ACS nano · 2025Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter.Nucleic acids research · 2024Article
- Molecular Mechanisms Involved in the B Cell Growth and Clonogenic Activity of HIV-1 Matrix Protein p17 Variants.Viruses · 2024Article
- Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy.International journal of molecular sciences · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 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
- Article
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association.Journal of chemical information and modeling · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent.Journal of chemical theory and computation · 2023Article
- Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.Journal of chemical information and modeling · 2023Article
- Performance analysis of DNA crossbar arrays for high-density memory storage applications.Scientific reports · 2023Article
- Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.Journal of chemical information and modeling · 2023Article
- Rational Design of de novo CCL2 Binding Peptides.Advanced theory and simulations · 2023Article
- Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function.Frontiers in chemistry · 2023Article
- Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA.The journal of physical chemistry letters · 2022Article
15 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundThe structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA.
methodsMolecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms.
resultsThese molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale.
conclusionsWe can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. GENERAL SIGNIFICANCE: With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics.
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