VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 16 2006 - 22:00:44 CST

Can you email me the file size reported by 'ls -l' as well as
the atom count, and the complete messages printed by VMD when
you load the file? That should provide me with enough details to
glean some more useful information.

  John

On Thu, Nov 16, 2006 at 07:55:01PM -0800, Neelanjana Sengupta wrote:
> I am running it on our public cluster, which runs Red Hat Linux (I need to
> check what version). It is running VMD 1.8.5
>
> On 11/16/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> >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
> >
>
>
>
> --
> ****************************************
> 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