VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Aug 05 2003 - 22:32:21 CDT

Hi John,

I am running the vmd on another machine by forwarding the graphical
display on my station. Moreover I understood that the machine (it is a
mass storage) moves files biger than a certain size on tape automatically
so when the files are used they are read from the tape. Do you think that
this delay causes the trouble I've got?

I am using this opportunity to ask another question:
I want to retrieve the z coordinate of a couple of atoms from the NAMD
generated dcd (trajectory) file. What is the way to do this (I wrote out
the trajectory in binary format)?

Thank you,
Ioana

On Tue, 5 Aug 2003, John Stone wrote:

>
> Ioana,
> That looks like a low level error in dmconvert. The "dgl" error
> sounds like it may require that you be running it locally on the
> console of the SGI, since "dgl" is the SGI way of doing their
> proprietary graphics stuff, potentially employing hardware
> video codecs etc. Did you run all this on the console of
> your SGI?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 05, 2003 at 04:04:15PM -0700, Ioana Cozmuta wrote:
> > Hi,
> >
> > I am trying to make an mpeg (dmconvert) movie using the vmdmovie menue but
> > I get the following error.
> >
> > Converting frames from rgb format to ppm... Converting frames to SGI
> > MPEG-1 video format dmconvert -v -f mpeg1v -p video,rate=24 -n
> > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm,start=0,end=9,step=1
> > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm
> > /u2/ioana/calibr_meas/1K/diff_1K/movieK.mpg
> > bgerror failed to handle background error.
> > Original error: -------- Scanning input ... dgl error (read): <bad
> > errno = 0>
> > Error in bgerror: invoked "break" outside of a loop
> >
> > Does anyone have any idea what is causing this error?
> >
> > Thank you,
> > Ioana
>
> --
> 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
>