VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Wed Aug 22 2007 - 15:36:09 CDT

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Hi!

Mark Zottola wrote:
> After loading a GROMACS-generated pdb file and trajectory into VMD I
> issue the command "all within 10 of resid 247". This results in a
> "ball" of protein atoms and water molecules - all well and good.
> However, I also get a "ball" of waters (only water) separate and
> distinct from the expected and desired selection. Unless this is a
> bug, I am obviously missing something.

I can only guess on that: maybe there are atoms labelled "resid 247" in
the protein, and also some outside? Just test which atoms are shown when
you just select "resid 247".

> Second, I would like to watch the dynamics of that previous
> selection. Since the ball of unwanted waters is far from the
> protein/solvent of interest, I figured I would let the simulation run.
> However, What I apparently observe is the motion of all the waters
> slowly diffusing away from their original position. Is there any way of
> simply focusing in on a region of the ensemble and simply watching the
> atoms that exist /within that region/?

To do that, you need to activate
Main-> Graphics-> Representations-> Trajectory-> "Update Selection Every
Frame"

Cheers
        Olaf
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