title: Molecular dynamics trajectories of protein folding
author: shinji iida
description: 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. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78, 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. J. Chem. Phys. 126, 014101 (2007)) Time step : 2 fs gromacs-2020.6 