VMD-L Mailing List

From: Scott Stagg (scott.stagg_at_biology.gatech.edu)
Date: Thu Sep 11 2003 - 15:07:33 CDT

I am trying to make a movie of my simulation where in each frame the
protein is superposed back on the first frame. No problem there except
that in some frames a ligand that is bound to the protein is wrapped
around the periodic boundary while the protein is not. So in the movie,
it looks like every so often the ligand jumps off the protein. Is there
any way to get that molecule back in its proper place?It is a constant
pressure simulation, so the box size changes, which I would imagine
makes it hard to wrap the ligand back around. Any suggestions?

Thanks,
Scott Stagg