VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 13 2004 - 15:12:08 CDT

Hi,
  I've attached a correctly formatted xyz trajectory as an example.
It has 5 frames in it. Let me know if you need more help getting yours
working.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 13, 2004 at 03:02:27PM -0500, Jayendra Balasubramanian wrote:
> Hi,
> 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?
>
> Thanks,
> Jayendra.
>
> > 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
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> 

-- 
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: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078