A simple Python script, based on Pandas and MDTraj, for tracking the temporal evolution of secondary structure along a MD trajectory.
Arguments
-p --top Topology file. If you want a result per chain, use a pdb file.
-t --traj Trajectory file. Output from MD simulation
-s --str Stride. Value must be an integer.
-d --dir Working directory. Default is current directory.
-v --ver Script version
Example: python PySSTraj.py -p run.gro -t traj_prod.xtc -s 1