期刊
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
卷 1850, 期 5, 页码 1041-1058出版社
ELSEVIER
DOI: 10.1016/j.bbagen.2014.09.007
关键词
DNA dynamics; Nucleic acid; Base pair fraying; Convergence; Reproducibility; Molecular dynamics
资金
- NIH [R01-GM081411]
- NSF [CHE-1266307]
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [0910735] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1266307] Funding Source: National Science Foundation
Background: The 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. Methods: Molecular 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. Results: These molecular dynamics simulations including one of the longest simulations of DNA published to date at similar to 44 mu s surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the similar to 1-5 mu s timescale. Conclusions: We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the mu s 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 GPO 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. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).
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