From: Axel Kohlmeyer (
Date: Fri Jan 16 2009 - 14:00:00 CST

On Fri, 16 Jan 2009, AA wrote:

AA> I'm writing my own software, and I want to be able to visualize what I have on a grid. The grid is fixed, but the number and types of atoms/molecules at each site changes, so some atoms enter or leave the system permanently.
AA> The XYZ format looks like it would match what I want to do, so I programmed that up... however, according to this page:
AA> it reads the atom labels ONCE, and then never again.
AA> I need to be able to change the labels for each step.
AA> Is there a way to do this with VMD?
AA> Any relevant or alternative suggestions are welcomed.


please have a look through the mailing list archives for
discussions on this subject. there are a number of ways
how you could do this, however the basic problem is that
VMD currently assumes that the number of atoms and their
identity does not change. this allows for much higher efficiency
in terms of memory consumption and speed for this - quite
typical - scenario.

the workaround directly available in VMD would be this:

where you have to create a seperate file for each step
and then load them into individual "molecules".


AA> thanks!
AA> Amos.

Axel Kohlmeyer
   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.