Molecular dynamics trajectories of protein folding

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