VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 24 2004 - 10:57:41 CDT

Hi,

On Fri, Sep 24, 2004 at 09:24:29AM +0200, Pär Olsson wrote:
> Hi all,
>
> At the moment vmd only reads the atom names for the first frame in an
> xyz-file. Is there some way to force vmd to re-read the names and plot
> the atoms accordingly?

No. You can load such structures as separate "molecules" in VMD, but
you cannot load them as a trajectory since VMD demands that the atom
count and types remain fixed over the course of a trajectory at the
current time. It is clear that there's increasing demand to support
this type of simulation, but I haven't had an opportunity to look at
recoding VMD to handle this case, it will be a formidable problem,
particularly from the performance point of view.

> Example: I have a Monte carlo code where atoms in a lattice exchange
> places and I want to animate the process.
> The xyz-file will look like this (minimalistic version):

[...]

Probably the best way to get what you want is to load these as separate
molecules in VMD and use a script to animate them by toggling the molecules
on/off one at a time in sequence. This is painful, but it's the only option
if you really want things like atom labels, names, and all of that to be
correct for a given structure in your simulation. If you just wanted to
_color_ the atoms, you could ignore their names and assign time-varying
values to the "User" field in VMD and color them by "User". This would
allow you to color given atom types with specific colors and yet have
them change over time. This too would require some scripting however.

> As it is now, vmd will treat this as if nothing has happened between the
> frames. Solution? (...and no, I can't manually exchange the order of the
> lines, not in a realistic example with 200 000 atoms in each frame...)

What simulation program are you using to generate these trajectories?
It might be possible to change your simulation program to generate
trajectories that are easier for VMD to work with. Ultimately though,
we may have to make VMD cope with this type of trajectory by eliminating
some of the assumptions that VMD currently makes about the consistency of
the molecular structure over time.

  John Stone
  vmd_at_ks.uiuc.edu

>
> Cheers!
> Pär
>
> --
> Pär Olsson
> Department of Neutron Research & Condensed Matter Theory Group
> Ångström Laboratory
> Uppsala University
> email: olsson_at_tsl.uu.se
> Phone: +46-18-471 3254
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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