From: Axel Kohlmeyer (
Date: Thu Mar 10 2011 - 19:08:44 CST

dear eric,

On Fri, Mar 11, 2011 at 8:12 AM, Eric Germaneau <> wrote:
> Dear all,
> I'm working with inorganic crystal structure and I don't want vmd to compute
> bonds when I load structure files.
> I know the command  mol new filename autobonds 0, but we have to do it each
> time we laod a new structure.
> And what if I run .vmd filename in a unix shell.
> So, I'd like to know whether it's possible to set something like "autobonds
> off" by default in .vmdrc file.

not at the moment. but it looks like it would be a good feature
to add to the "mol default" canon.

the way you i would work around this would be to write a little
wrapper script, e.g. vmd-nobonds:


tmpfile=`mktemp /tmp/vmd-load.XXXXXXX`

echo "mol new $1 autobonds 0 waitfor all" >> $tmpfile
vmd -e $tmpfile
rm -f $tmpfile

this is only a simple version that handles a single file,
but with a little bit additional shell scripting, it can be easily
adapted to handle multiple files and other startup flags
transparently. ;)


> Thanks,
>                     Eric.
> --
> Be the change you wish to see in the world
> — Mahatma Gandhi —
> Dr. Éric Germaneau
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
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Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.