From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Fri Feb 10 2012 - 08:49:55 CST

Dear Charbel

This is the command
vmd -dispdev none
or
vmd -dispdev none

for your purpose do you know "bincoordinates"? Have a look in the NAMD
guide.
You don't need a pdb file, NAMD can read its own binary files.

Anyway, what do you mean by script? Bash script? Does something like
this look fine?

#!/bin/sh

###############
#a lot of shell scripting here
####################

# VMD call
echo "animate read coor filename.coord waitfor all ;
[atomselect top all] writepdb filename.pdb
" | vmd -dispdev none -eofexit

###############
#a lot of more shell scripting here
####################

exit 0

Be careful to escape " and $

To answer to your second question, look to this option "binaryoutput" in
the manual. Try if setting it as "no" is what you are looking for. But
you lose accuracy in case you'd like to restart your simulation.

On 10/02/12 11:26, R. Charbel Maroun wrote:
> Hello VMDers,
>
> Is it possible to run VMD in stand-alone (non-graphical) mode ? Within
> a script, I just want to be able to read a .coor NAMD binary file and
> save it as an ASCII
> .pdb file for further use in NAMD.
>
> An alternative question is, how can I get NAMD to write a .pdb file
> after an MD ? I tried writepdb <filename> in an NAMD script and it
> gives the following error:
>
> ------------- Processor 7 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Setting parameter writepdb from script failed!
>
> I use VMD 1.9 and NAMD 2.8.
>
> Cheers,
>
> CM
>
>
>
> ----------------------------------------------------------------
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>
>

-- 
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