VMD-L Mailing List

From: Nicolas CHARVIN (Nicolas.Charvin_at_univ-savoie.fr)
Date: Mon Apr 04 2005 - 05:31:31 CDT

>To load it, get the files in that directory, then execute VMD with:
> vmd -e virus-simple.vmd
>
>Does VMD successfully render the structure on your machine?

yes, it loads very smoothly. I get 2.8 fps in VDW mode, and 62 fps
(maximum) in lines mode.
By the way, the "Determining bond structure from distance search" seems to
perform very quickly for a 395250 atoms molecule.

When I try to load my "test" big molecule ( 640,000 atoms, grab it at
http://www.univ-savoie.fr/labos/lmops/people/ncharvin/bazar/BigConfig.zip)
, I get a "MolAtom #### : Exceeded maximum number of bonds (8)" error
during "Determining bond structure from distance search" phase, and it
seems to loop forever on Molatom number, which is new (vmd 1.8.2 crashed).
By the way, Qmol can read and render it fairly smoothly.

I do not know much about this big molecule, and about bonds and structure,
stuff like that, so maybe theres are more than 8 bonds. That may explain
why VMD refuse to load it.

[...]

Heyy ??? I've just generated a solvation box of 1.3 Million atoms, with
"Solvate Plugin".
I try to load solvate.pdb
(http://www.univ-savoie.fr/labos/lmops/people/ncharvin/bazar/solvate.zip) ,
WITHOUT using solvate.psf file, and it works perfectly, with the
"Determining bond structure from distance search" phase.

It seems something is wrong with my BigConfig.pdb...

Any ideas ?

Thanks in advance

nicolas 

--
Nicolas.Charvin_at_univ-savoie.fr
LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
Bât IUT - Université de Savoie
73376 LE BOURGET DU LAC CEDEX
Tel: 04-79-75-86-53
http://www.univ-savoie.fr/labos/lmops