I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do
atomselect it takes a frame identifier as an argument. With MDAnalysis I saw this:
with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb: for ts in u.trajectory: pdb.write(u)
However, I am not sure how to use it in a complete script.