From: Axel Kohlmeyer (
Date: Wed May 18 2011 - 08:23:49 CDT

On Wed, May 18, 2011 at 8:04 AM, Jorgen Simonsen <> wrote:
> Hi all
> I have organized my output in different directories and would like to
> use some packages within vmd to analyse the output - I have naively
> put my script together like this,mrun
> #!/bin/bash
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet.scr
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet2.scr
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet3.scr
> the tet.scr contain the following
> for { set i 1 } { $i $\leq$ $nf } { incr i } {
> $sel frame $i
> $sel move [measure fit $sel $frame0]
> puts $outfile "[measure rmsd $sel $frame0]"
> quit
> where 2 and 3 are modifications. If I do manually go to a directory and
> source
> it works fine but if I loop thorugh it - it opens and immediately
> quits the application.

VMD will begin script processing as soon as
the loading of the file data has commenced,
since the loading of coordinate data from the
command line does not imply "waitfor all".

you'd have to load the coordinates as part of the
script. why run this as separate scripts in the
first place? the overhead of launching VMD is
huge. why not just do the looping/scripting from
inside VMD. tcl is a much better script language
than shell script...


> Thanks,

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.