Index of /dali/Trp_Cage

Molecular Dynamics Data Set for the Mechanism of A Protein Folding Reaction

Contact: Aaron Dinner, Professor at Department of Chemistry, University of Chicago

Name	Last modified	Size
Parent Directory		-
Featurized_Trajectories/	10-Feb-2021 17:12	-
MDP_Files/	10-Feb-2021 17:12	-
Python/	20-Apr-2021 09:54	-
Trajs/	10-Feb-2021 17:12	-
TrajsHelix/	10-Feb-2021 16:47	-
_README.txt	12-Mar-2021 18:03	841

Data:

64 starting points are indexed (p,q) in a grid in the full RMSD/3-10Helix RMSD space in the files /Trajs/s0pi0q/.
In each of these files are 15 .xtc files each containing a 30 ns trajectory launched from the same starting point.
2 Additional trajectories are contained in a similar fashion in the folder /TrajsHelix with the starting points from a grid in 3-10 Helix RMSD/alpha helix RMSD space.

MD parameters:

Gromacs Molecular dynamics parameters, topology files, index files, force field files, and a starting .gro file are included in /MDP_Files.

Python files:

Functions for carrying out the DGA calculations and TPT estimators are contained in /Python/DGA.py. An example jupyter notebook is provided as well which runs the DGA and TPT estimators on the featurized trajectories and CVs contained in /Featurized_Trajectories.