From: Leonardo Trabuco (
Date: Tue Nov 09 2010 - 08:01:15 CST

Hi Steve,

On Tue, Nov 9, 2010 at 2:11 PM, 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?

You can set the 'user' field (per-atom, per-frame) and make selections
based on that instead. See


> Thanks in advance for any help,
> Steve

Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany