VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Nov 09 2010 - 08:06:58 CST

Hi,

you could save this property in the user
field<http://www.ks.uiuc.edu/Research/vmd/current/ug/node88.html#table:ug:keywords>of
each water molecule.Then you could color or display the solids
differently.

something along the lines:

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

Regards,
Ajasja

On Tue, Nov 9, 2010 at 14:11, Stephen Cox <stephen.cox.10_at_ucl.ac.uk> 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
>