VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 26 2008 - 05:12:34 CST

roberto,

this is a well known design feature of VMD (to be more efficient
for huge systems of regular classical MD trajectories) and much
discussed on this mailing list. please search through
the mailing list archives for a selection of suggestions
on how to handle this situation with VMD.

cheers,
   axel.

On 11/26/08, Roberto Gaspari <Roberto.Gaspari_at_empa.ch> wrote:
> Good morning to all,
> I've produced a trajectory with xyz files of a system with three different
> atoms. Each frame of the trajectory can be displayed correctly when loaded
> alone and all the three atoms have a different colour. When I cat the frames
> in a single trajectory file, and load this file to VMD, the animation starts
> correctly, but from the second frame on, the colours don't match anymore
> the correct atoms.
> An example of my trajectory file would be:
> 3
>
> Fe x1 y1 z1
> Cu x2 y2 z2
> Au x3 y3 z3
> 3
>
> Fe x4 y4 z4
> Fe x5 y5 z5
> Au x6 y6 z6
>
> .............
>
> PS My trajectory frames have a constant number of overall atoms, but the
> number of individual species changes at every step.. maybe this can be a
> problem?
>
> Best Regards,
> Roberto Gaspari
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.