From: Ajasja Ljubetič (
Date: Tue Nov 09 2010 - 08:06:58 CST


you could save this property in the user
each water molecule.Then you could color or display the solids

something along the lines:

set sel [atomselect top <solid water indices here>]
$sel set user 1


On Tue, Nov 9, 2010 at 14:11, Stephen Cox <> wrote:

> 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