VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Apr 10 2003 - 20:05:39 CDT

Hi,

It worked well if I loaded the prmtop file and the dcd trajectory
Still I do not understand why I've got that both structures were centered
in zero although they were shifted :)

Ioana

On Thu, 10 Apr 2003, John Stone wrote:

>
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>