VMD-L Mailing List

From: Stephen Cox (stephen.cox.10_at_ucl.ac.uk)
Date: Tue Nov 09 2010 - 07:11:58 CST

Hi,

I am trying to visualize the freezing of ice and I have an external program
that specifies which molecules may be defined as solid. Obviously when going
from liquid to ice the number of "solid" particles changes and this poses a
problem when reading in a trajectory coordinate file as all atom descriptors
(name, mass etc) are read in only from the first frame and vmd doesn't allow
variable number of atoms in an xyz file (for example). I have tried multiple
molecule animation but this seems impractical for long trajectories...

Is there any way that I can label the atoms defined as solid at each frame
so that vmd can recognise them? Alternatively, could I script an atom
selection on a frame by frame basis?

Thanks in advance for any help,
Steve