From: Aaron Oakley (aarono_at_uow.edu.au)
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?
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