VMD-L Mailing List

From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Mon Sep 04 2006 - 13:01:42 CDT

Hi Axel

Thanks for your comments

Some of the script is a leftover from a file initially for submitting namd
jobs. Those parts shouldn't be causing any problems though.

The jobs are being launched from a master server on the node selected by pbs,
thats why the ssh. As far as I understand pbs just returns the resource info,
it's then up to the rest of the script and the programs it calls to make use
of that.

As for the loading order, the coordinates are indeed the first frame.

I don't get any errors using ">&". pre_rmsd_per_res prepares various files and
variables before calling bigdcd. I can post it, but as far as I know it
shouldn't be the cause of the problem. If I run the "ssh..." command (or the
script) directly all works fine. The problem comes when calling from the
script via qsub. Using sleep doesn't help either, it seems to interfere with
the repeated frame loads from bigdcd and isn't executed after bigdcd.

I'd still like to know why vmd simply when returnig control, since the
intended quit command which get's called at the end of bigdcd is never even
reached?

regards
gordon 

-- 
If you want to know what God thinks of money, just look at the people he 
gave it to. 
	
	-- Dorothy Parker
Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria