From: Jérôme Hénin (
Date: Tue Nov 09 2010 - 08:28:49 CST

Hi Steve,

You can encode that information in the "user" field, which is stored
for each frame. It can be set by a script for the whole trajectory at
once, then used for visualization.


On 9 November 2010 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