Re: keeping a protein in a solvation box

From: Aaron Oakley (
Date: Tue Jun 12 2012 - 18:45:19 CDT

You could use collective variables to remove the rotation/translation component of your macromolecule.


On 13/06/2012, at 8:44 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 : Mon Dec 31 2012 - 23:21:38 CST