Re: keeping a protein in a solvation box

From: Eduard Schreiner (
Date: Tue Jun 12 2012 - 18:19:11 CDT

sounds like the protein just diffuses. since you are using pbc, the
protein is solvated, given the dimensions of the box are larger than
those of the protein. The box you see after wrapping is generated by
wrapping molecules in such a way, that the individual molecules don't
get broken. This way, it may look like a part of the protein sticks
out of the box. Check the manual for the behavior of the wrapall
parameter. Simulate longer, and once it is about to move completely
out of the box, it will be wrapped back into the box. why should one
change the physics by fixing atoms just so it looks nice?


On Wed, Jun 13, 2012 at 12:44 AM, Dr. Eddie <> wrote:
> Hi all,
> What is the best way to keep a protein inside a solvation box?
> With wrapwater and wrapall on my protein still climbs out of the box
> (presumably still experiencing solvation due to periodic boundary
> conditions, but I can't be sure). I'd like the protein to stay in the box.
> Should I fix one single atom in the protein? Is there a better way than just
> making an enormous box?
> Thanks,
> Eddie

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:07 CST