Re: Aligning structures

From: Peter Freddolino (
Date: Thu Mar 09 2006 - 21:37:05 CST

Dear Richard,
you can align multiple frames of a trajectory using the attached tcl
script. To use it, do the following:
source align_frames.tcl
align_frames molid seltext

This will go through the entire trajectory in molecule molid, align each
frame of it to the first (it only aligns the selection of seltext,
usually "all") and outputs the rmsds of each step to the file rmsd.dat.
The script is fairly short so you should be able to modify it to suit
your needs.

Richard Wood wrote:

> Hi all,
> Is there a way to align all the frames of a dynamics calculation using
> VMD? I know that one can open two or more molecule files and do an
> alingment on them, but I need to know if I can do this with a dynamics
> trajectory having 100 frames or more. I need to align all the
> structures and then calculate RMSD's. Any help will be most appreciated.
> Richard
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030

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