From: Kooser, Ara S (
Date: Tue Apr 13 2004 - 15:46:35 CDT


   John provided a script that removes bonds after the .xyz is loaded. I ran
a boehmite cell .xyz trajectory this morning. The format for the trj. File
was something like:

<atom type1> x y z
<atom type2> x y z
<atom type3> x y z
<atom type1> x y z
<atom type2> x y z
<atom type3> x y z


Hope that helps.


-----Original Message-----
From: Jayendra Balasubramanian []
Sent: Tuesday, April 13, 2004 2:02 PM
Subject: Re: vmd-l: Viewing MD trajectories

   I wrote the xyz file as a concatenated set of xyz files like you
said with title lines and number of atoms emitted after each time
step, but vmd still does'nt read the number of frames. In fact if I
write it out as a continuous file with the title and number of atoms
written only at the beginning of the file vmd reads the number of
frames but it tries to draw bonds between all the atoms which results
in two things :

    1.The resulting image is very messy - I don't want the bonds
because the system is just a set of individual atoms.
    2.There is an error message in the command line window which says
maximum no. of bonds (8) exceeded.

     Any suggestions as to how I can make vmd read the xyz file as
just a set of atoms and show the trajectories by just letting the
atoms move in space after every time step?


> 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
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: Phone: 217-244-3349
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