From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 26 2006 - 14:48:11 CDT

Hi Sandeep,
  If you want to upload your XTC file to the VMD Public project on
BioCoRE, I'll be happy to take a look at it. I'll also need the
matching PDB, or other file(s) that go with the XTC as well.
  http://www.ks.uiuc.edu/Research/vmd/alpha/

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 26, 2006 at 01:59:50PM -0400, Sandeep Prakash wrote:
> Hello all,
>
> I am having this problem in VMD where every time I run .xtc file to
> visualize the simulation I am running, bonds appear to form between
> molecules at random. When I look at the snapshots, there seem to be no such
> bonds forming. Also, when I looked at the simulation in some other
> visualization programs, they appear okay. I am attaching a picture of how
> the simulation appears. Please suggest something.
>
> Thank you
>
> Regards
>
> Sandeep
>
>
>
>
>
> Sandeep Prakash
>
> Graduate Research Assistant
>
> Chemical Engineeering
>
> 147-E Randolph Hall
>
> Virginia Tech
>
> Blacksburg, VA - 24061
>
> Phone: (540) 231- 2596
>
>
>

-- 
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