From: Peter Freddolino (
Date: Tue May 29 2007 - 16:20:56 CDT

Hi Alison,
to start with, you may want to look at the RMSD Trajectory Tool plugin
which lets you align frames and different structures based on certain
selections and calculate the resulting RMSDs. This is usually a good
step prior to other types of analysis as well. You can find it under the
Extensions->Analysis menu of VMD.


Alison Grinthal wrote:
> I'm new to VMD and am wondering if someone can provide advice on the
> best way to do the following:
> I have a trajectory file from a pulling simulation, and I'm trying to
> compare the structural details of the initial, early, and final
> stages. So first I'm wondering how to overlay structures from
> different frames, while specifying which segment to base the alignment
> on. I'd also like to compare the structure of a given trajectory frame
> with the published structure of the same protein crystallized in
> complex with another subunit (which isn't present in the simulated
> structure's psf file; it's a different pdb file).
> More specifically, the protein is composed of sequential repeats, and
> I'd like to analyze how the orientation between adjacent repeats
> changes with pulling. To do this, I'd like to look at 2-repeat units
> from different frames, but align them based only on the first repeat,
> so I can see how the orientation of the second repeat changes relative
> to the first.
> Thanks very much for any advice.