VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 10 2005 - 14:53:09 CDT

Hi,
  I hadn't realized that anyone would produce XYZ files of the size
you're making. (It's an ASCII file format, so it's ill-suited for
use as a trajectory file format...) I can certainly add in code to
allow XYZ files larger than 2GB to be written, it's quite easy, it just
never occured to me that anyone would do it since there are MUCH more
compact trajectory formats available. What is the ultimate trajectory
file format you're converting to by the way? Maybe there's a more direct
route than by making a huge XYZ file? If you want to try a test build of
VMD with a LFS-enabled XYZ writer, let me know and I can build one for you.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 06, 2005 at 11:43:14AM +0100, Kaihsu Tai wrote:
> I am using the following procedure suggested by Justin in
> our project; but with VMD 1.8.2, the XYZ file does not seem
> able to exceed 2 gibioctets (the largest file generated
> being 2147483647 octets). Is it possible to link with
> large-file support in future versions?
> http://www.ece.utexas.edu/~luo/linux_lfs.html
>
> Cheers. (I will upgrade to 1.8.3 soon.)
>
> Justin Gullingsrud, 2004-12-13 08:24:40-0800:
> > VMD can do this. A quick way to do it in batch mode is to create a
> > script with the lines
> >
> > animate write xyz $argv waitfor all
> > exit
> >
> > and run vmd with the command
> >
> > vmd -dispdev text alanin.psf alanin.dcd -e script.tcl -args alanin.xyz
> >
> > I've tested this with VMD 1.8.2; newer versions of VMD should work as well.
> >
> > On Mon, 13 Dec 2004 16:11:48 +0000, Kaihsu Tai <kaihsu_at_biop.ox.ac.uk> wrote:
> > > BioSimGrid needs to read in trajectories in CHARMM DCD
> > > format. This sounds trivial, but actually is quite
> > > complicated to make reliable.
> > >
> > > After trying a few things, it seems the most reliable way is
> > > to convert the DCD files into XYZ format one frame per file,
> > > and then read them back in (we are doing exactly this for
> > > Gromacs).
> > >
> > > Does anybody have an API in the C language (or Python) that
> > > can do something like this? (Web searches have been
> > > fruitless.)
> > >
> > > http://bugs.biosimgrid.org/show_bug.cgi?id=176 

-- 
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