VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 16 2006 - 21:49:09 CST

What version of VMD are you using and what platform are you running on?
I'm curious how you'd get a weird file size measurement like that,
particularly from a rewritten DCD file.

  John

On Thu, Nov 16, 2006 at 07:44:14PM -0800, Neelanjana Sengupta wrote:
> Hi,
>
> I have a globular protein in a box of solvent. My simulation is performed
> without the wrapAll on (as I am interested in diffusion). However, I want to
> check the actual number of solvation molecules (within say a 4 angs
> solvation layer). I also need their coordinates (changed as per the minimum
> image convention).
>
> Hence, I apply the pbcwrap.tcl script, and then re-write a new .dcd file for
> my trajectory. This new .dcd trajectory is what is issuing this warning...
>
> Your comments as highly appreciated.
>
> On 11/16/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> >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
> >
>
>
>
> --
> ****************************************
> 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