VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 11 2003 - 14:56:41 CDT

Ioana,
  If you provide me with the files that cause the behavior you
describe I can have a closer look. There are too many unanswered
questions for me to give you a definitive answer without seeing the
files at this point.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 10, 2003 at 06:05:39PM -0700, Ioana Cozmuta wrote:
> 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
> > 

-- 
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