From: Axel Kohlmeyer (
Date: Wed Aug 22 2007 - 14:12:59 CDT

On Wed, 22 Aug 2007, Mark Zottola wrote:

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

you are missing the fact that resid is the residue number that
VMD reads from the .pdb file and my guess is that you have the
same residue number twice (once in the protein and once in the
water). try using "within 10 of (resid 247 and protein)".

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

check out the trajectory tab in the graphical representation window.
there is a box 'update selection every frame' that you need to

MZ> Thanks!
MZ> Mark

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.