Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

• Published in: Biochimica et biophysica acta Vol. 1850; no. 5; pp. 1041 - 1058
• Main Authors: Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2015
• Subjects: Algorithms; B-DNA; Base pair fraying; Convergence; DNA - biosynthesis; DNA - chemistry; DNA dynamics; DNA Repair; DNA Replication; molecular conformation; Molecular dynamics; Molecular Dynamics Simulation; Motion; Nucleic acid; Nucleic Acid Conformation; Principal Component Analysis; Reproducibility; Reproducibility of Results; Structure-Activity Relationship; Time Factors; Transcription, Genetic; Molecular dynamics; Base pair fraying; DNA dynamics; Reproducibility; Nucleic acid; Convergence

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...