VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 14:44:06 CDT

Lubos,
  I haven't seen this, it might be some periodic cell type that
VMD doesn't understand or some other issue. If you can provide me
with pared down structure and trajectory files I'd be happy to take a look.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 04, 2005 at 05:59:44PM +0200, Mgr. Lubos Vrbka wrote:
> hi guys,
>
> i'm trying to view trajectory from gromacs using vmd. the system is a
> slab with 6-center water molecules (O, H, H + 3 extra points). there is
> one strange thing. after some time, the trajectory gets distorted - it
> looks like extrapoints are not wrapped. when i display only oxygens and
> hydrogens, then it's ok.
>
> has anyone encountered this "feature"?
>
> when displayed in ngmx, it seems to be ok, however i'm not sure since
> extra points are not connected to the "mother" atom there...
>
> thank you in advance for any hints. best regards,
> lubos
>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
> ..................................................... 

-- 
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