VMD-L Mailing List

From: tom keyes (keyes_at_chem.bu.edu)
Date: Wed Oct 03 2001 - 16:37:49 CDT

Hello,
  I just got VMD running under OSX with Xtools, not Xfree86, and it seems
fine so far. I'm a highly non-biological physical chemist simulating
supercooled simple liquids and I want to animate MD trajectories. I usually
write them as xyz for each atom, repeated for each time step in the same
file. I added minimal PDB 'boilerplate' to a single configuration, gave it
a .pdb extension, chose 'pdb only', and VMD displayed it nicely. I then
saw the sentence in the User's Guide "...while PDB....files were designed
to contain only one coordinate set, multiple files can be concatenated into
one larger file to create a makeshift trajectory which is recognized by
VMD." Thus I modified a FORMAT statement to add the pdb stuff to the xyz,
and now I get a single pdb file repeated over and over in the same big
file, differing only in xyz for each time step. However this did not work,
VMD stalls on 'loading molecule'.
 So, am I on the wrong track? Do I need a different method of
concatenation? Could someone provide more detail on what I quoted from the
Guide? I've found a script 'animatepdbs' which apparently will animate a
sequence of distinct pdb files, one for each config, and it will be trivial
to write a lot of little files instead of one big one, or I suppose it
could be modified to pick the date for one time step out of the big file.
However what i tried first seems simplest. Can something like that work?

Thanks
Tom Keyes