Force field comparison: Amber, GROMOS, CHARMM, OPLS скачать в хорошем качестве

Force field comparison: Amber, GROMOS, CHARMM, OPLS

Force field comparison: Amber, GROMOS, CHARMM, OPLS: Comparison of secondary structure formation using different force fields in microsecond molecular dynamics simulations. All simulations were started from the same initial conditions. We tested the following force fields: Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27 and OPLS-AA/L What is in the movie: The movie spans 0-10 and 990-1000ns of the 1000ns trajectory. For clarity, water, ions and hydrogens are not shown and rotation and translation of the peptide has been removed. Secondary structures (mostly visible in the 990-1000ns part) were colored as follows: yellow - β-sheet (arrows indicate chain direction) purple - alpha helix blue - 310 helix white - coil Interaction between D77 and T80 typically precedes hairpin formation. This interaction is formed in the first 10ns in the Amberff99SB*-ILDN trajectory. See also: 1. Force field comparison: Single peptide using Amber99SB*. http://www.flickr.com/photos/softsimu... 2. Microsecond atomistic MD simulation: Transition of the 9-mer mouse Neh2 peptide from an extended to beta-turn conformation. http://www.flickr.com/photos/softsimu... 3. Convergence of the 32-mer mouse Neh2 peptide to a bound-state-like β-turn conformation http://www.flickr.com/photos/softsimu... Computational resources: SharcNet References: 1. Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations, Elio A. Cino, Wing-Yiu Choy and Mikko Karttunen, accepted for publication in JCTC. http://dx.doi.org/110.1021/ct300323g 2. Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response, Elio Cino, Jirasak Wong-ekkabut, Mikko Karttunen, Wing-Yiu Choy,PLoS One 6, e27371 (2011). http://dx.doi.org/10.1371/journal.pon...