VMD-L Mailing List

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon Nov 24 2003 - 15:46:21 CST

Madhuri,
I assume you have a psf also if you were able to run a trajectory the
protein. If so, you can load the dcd into the psf in VMD and source the
following tcl script.

Note:
1. Changing the 'choice' variable will allow you to include/exclude parts
of the protein in the rmsd.
2. This script calculates the rmsd w.r.t. the 0th frame.

set choice "protein and backbone"
set filename protback
set outfile [open rmsd-$filename.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "$choice" frame 0]
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
  set sel [atomselect top "$choice" frame $i]
  $sel move [measure fit $sel $frame0]
  puts $outfile "[measure rmsd $sel $frame0]"
  }
close $outfile

-Tim

On Sun, 23 Nov 2003, Madhuri Agashe wrote:

> Is there a way to get the RMSD data for a dynamic simulation using VMD??
> I have the pdb file and the dcd for the simulation.
>
> -Madhuri
>
>
>