title: Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).
abstract: 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 ~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.
  
  
  CONCLUSIONS
  We 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Galindo-Murillo
authors.affiliation: Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Roe
authors.affiliation: Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA. Electronic address: tec3@utah.edu.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D000465:Algorithms; D004247:DNA / Q000096:biosynthesis / Q000737:chemistry*; D004260:DNA Repair; D004261:DNA Replication; D056004:Molecular Dynamics Simulation; D009038:Motion; D009690:Nucleic Acid Conformation; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D013329:Structure-Activity Relationship; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D004247:DNA
keywords: Base pair fraying; Convergence; DNA dynamics; Molecular dynamics; Nucleic acid; Reproducibility