VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 10 2003 - 19:30:22 CDT

Ioana,
  Do the coordinates in your DCD file differ substantially from those
contained in the PDB file you loaded? You can skip loading the PDB and
instead load the PSF file and then I would expect this to go away
since VMD will just use the coordinates from the DCD file then.
(If you load a PDB, then VMD loads the coordinates from the PDB
 as the first coordinate set, subsequent DCD loads just add additional
 frames. If you load a PSF, then VMD will only use the coordinates
 it finds in the DCD, but gets the bonding info from the PSF file...)

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 10, 2003 at 05:00:42PM -0700, Ioana Cozmuta wrote:
> Hi,
>
> There is something strange happening in VMD with my water box. I load the
> pdb file and it is centered in zero in the center of my screen as well,
> Then I load the namd generated dcd file and the first frame already
> shifts my whole water box into the left corner of the screen. If I
> calculate for this frame what is the center of the box it says zero.
> Any idea why this happens and how I could get around it?
> THanks a lot,
> Ioana 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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