VMD-L Mailing List

From: Kaihsu Tai (kaihsu_at_biop.ox.ac.uk)
Date: Thu Oct 06 2005 - 05:43:14 CDT

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