VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Nov 16 2006 - 21:55:01 CST

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
****************************************