Trajectory overlay with VMD

In Molecular Dynamics, especially when small fluctuations are involved, it can be helpful to display the snapshots contained in a trajectory all at once instead of viewing a movie. The same utility can be used, for example, to display the members of a structural cluster (you can generate clusters of structures using wordom).

This feature is usually achieved “by hand”, e.g., extracting all the snapshots of a trajectory into separate pdb files and then loading them all at once. A simple consequence of this, of course, is to have your hard-drive overfilled with redundant files.

Good for us, VMD is able to overlay in a single frame all the snapshots contained in your trajectory (thanks Riccardo for your message). Once your trajectory is loaded in (from command line):

vmd -f trj.dcd prot.psf

go to:

Graphics>Representations>Trajectory

in the field “Draw Multiple Frames” replace “now” with x:y:z where x is the first frame to display (starting from 0), y is the skip step, and z is the last displayed frame. In the case of a trajectory of 50 frames I would write something like:

1:1:50

That’s it! Your trajectory is overlayed.