Molecular dynamics trajectories of protein folding
收藏资源简介：
Molecular dynamics trajectories of protein folding are deposited for educational purposes. Currently, the following trajectories are available: Chignolin (five independent NVT simulations up to 1.5 micro-sec): `movie.pse` is a PyMOL session file of MD trajectories. `movie.mp4` is a movie file that shows you how a protein folds during simulation. xtc files (Gromacs compressed format) and corresponding tpr files. gro files for movie making Computational setting Amber ff99SB-ILDN for protein (Lindorff-Larsen, K. <em>et al.</em> Improved side-chain torsion potentials for the Amber ff99SB protein force field. <em>Proteins</em> <strong>78</strong>, 1950–1958 (2010)) TIP3P water model 0.1 M salt concentration NVT ensemble at 300 K with V-rescale thermostat (Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. <em>J. Chem. Phys.</em> <strong>126</strong>, 014101 (2007)) Time step : 2 fs gromacs-2020.6
