VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Feb 01 2005 - 13:59:08 CST

On Tue, 1 Feb 2005, Pascal Boulet wrote:

PB> Hello,

dear pascal,

VMD assumes that you have a constant number of atoms. it will
only read the atom labels (i.e. the atom structure) from the
first frame and then only read the coordinates.

PB> I am running grand canonical Monte Carlo simulations and store some
PB> structures into an XYZ multiframe file. Of course, the number of
PB> atoms/molecules may increase during the simulation.

PB> I couldn't visualise the trajectory file with VMD. Is there a way to do
PB> it?

one workaround would be to put each frame into a separate molecule
and then have a script toggle the on/off status of these molecules
properly. you can find an example for that at:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect4

another alternative (if only molecules of the same 'structure', e.g.
water molecules, are added/removed) would be to first take the frame
with the largest number of atoms, load this and then have all frames
in the whole .xyz file padded to that number of atoms and just put
the excess atoms at coordinates, far enough away from the rest,
so you can zoom in properly to not see them.

best regards,
        axel.
PB>
PB>
PB> Thank you for your help,
PB>
PB> Best Regards,
PB>
PB> Pascal
PB>
PB>
PB> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.