From: Ajasja Ljubetič (
Date: Fri Feb 10 2012 - 07:29:36 CST

> 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.
> Indeed it's possible:
use vmd -dispdev text -e "path to script to load and save your stuff"

More info here:

You could also consider using catDCD for this.

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:

 Try *binaryoutput no*
More info here