VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 16 2006 - 21:27:53 CST

Hi,
  For some reason your DCD file is larger than it should be for the
number of frames it contains. This message is a warning, and the DCD
plugin is telling you because there are cases where badly written
software can write a header that disagrees with the actual contents
of the file. In your case, the file is larger than it should be for
some reason. The DCD plugin can calculate down to the exact byte
how large the DCD file should be given the number of mobile and fixed
atoms, and the number of frames.
If the calculated size differs from the actual size, then the DCD
plugin divides the actual size by the atom counts to come up with
the number of frames that appear to be there.
The DCD plugin tells VMD what it thinks is the correct number after
checking various things, and that's what VMD will actually load.
The warning is for user's benefit that there's something fishy going on.
What program generated your DCD file? Do you have fixed atoms?
Anything else that's unusual?

  John

On Thu, Nov 16, 2006 at 07:15:38PM -0800, Neelanjana Sengupta wrote:
> Hi VMD users,
>
> When loading one of my system trajectories into VMD (a dcd file), I get the
> foll. unusual warning:
>
> dcdplugin) Warning: DCD header claims 4000 frames, file size indicates there
> are actually 5999 frames
>
> This is odd, as I KNOW for sure that my trajectory has 4000 frames. Can
> anybody throw light on this message? (I find it counterintuitive that VMD
> should make some estimate of the frame number based on the filesize. It
> seems too arbitrary, doesn't it? A lot depends on your type of system...)
>
> Thanks!
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> USA
> Phone: 1-949-824 9921
> email: sengupta_at_uci.edu
> **************************************** 

-- 
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