From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 17 2002 - 23:44:51 CST

Dear Ioana,
  If you load a CRD file for PBC, make sure you set the file
type to "crdbox" so that VMD knows that the CRD file contains
box information, otherwise there's no real way for it to know
whether the file has box info or not. That should cure your problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 17, 2002 at 09:15:55PM -0800, Ioana Cozmuta wrote:
> Hi vmd-users,
>
> I have a small trajectory generated with amber7 on SGI/IRIX (octane)
> machine. It is a cubical water box (L=20A) and I've run NVT dynamics
> using PBC. When I load the .crd file into VMD the bonds seem to be
> extremely stretched. However from the output it seems that there is
> nothing really wrong with the energy or with the run itself. I wonder if
> this is an artifact of the PBC visualisation in VMD?
>
> Thank you and Happy holidays!
>
> Ioana
>
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
> * NASA-AMES Research Center * "Gravitation can not be held responsible*
> * Mail Stop 230-3 * for people falling in love" *
> * Moffet Field,CA 94035 * *
> * phone: (650) 604-0993 * Albert Einstein*
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> ****************************************************************************

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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