VMD-L Mailing List

From: Mark Zottola (mzottola_at_gmail.com)
Date: Wed Aug 22 2007 - 14:28:53 CDT

I have two questions concerning VMD.

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.

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*?

Thanks!

Mark