VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Nov 16 2006 - 21:44:14 CST

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