VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 09 2004 - 20:12:46 CDT

Hi,
  If you want to view an XYZ file containing multiple timesteps, the
correct way to write it out is to write the file as a set of concatenated
xyz files, but not just by emitting all the atoms for all timesteps.
In other words, after each timestep, you must be sure to correctly
emit the atom count and title lines etc at each timestep as you would
if they were separate files. Does that make sense? If you do that
correctly, you'll see that VMD will load the xyz file as a trajectory
and will count up the total number of frames etc as you'd expect.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 09, 2004 at 04:46:48PM -0500, Jayendra Balasubramanian wrote:
>
> I am running MD simulations by writing my own Fortran code and I get
> the results as a set of position coordinates of all the atoms after
> each time step. These MD simulations are simulations of non-periodic
> atomic systems (NOT molecular systems or molecules) and I tried
> loading the position coordinates after every time step as an xyz file
> (with the positions of all the atoms in the system stored after every
> time step in a single xyz file). However gopen-mol draws bonds between
> these atoms and when I try to use the label function to hide the bonds
> it doesn't show any atoms or bonds in the list. Is there any way I can
> view the trajectories of these atoms as just atoms moving in space?
>
> Jayendra Balasubramanian. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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