VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 18 2011 - 10:42:53 CDT

On Wed, May 18, 2011 at 11:10 AM, Salvatore Mario Cosseddu
<S.M.Cosseddu_at_warwick.ac.uk> wrote:
> the script is not full... in this form it could not work. you at least
>
> need a "}" at the end of the for loop and setting some variables...

you misread the mail. the script code was meant to illustrate
the content of the tcl script code, not a wrapper around the
vmd invocations.

axel.

>
> what do you means by loops thorough it? something like
>
> for i in {1..3};
> do
> vmd -dispdev text -e tet.vmd ;
> vmd -dispdev text -e tet2.vmd ;
> echo $i;
> done
>
> because it should work if there's no bus in the tcl script and it finish
> with exit. May you post the full script?
>
>
> On 18/05/11 13:04, 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 mrun.sh
>>
>>  it works fine but if I loop thorugh it - it opens and immediately
>>  quits the application.
>>
>>  Thanks,
>
> --
> Salvatore Cosseddu
> PhD student
> --
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
> --
> email: S.M.Cosseddu_at_warwick.ac.uk
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.