Re: Behavior of explicit water beyond periodic boundaries

From: Dr. Eddie (
Date: Thu Dec 20 2012 - 11:42:31 CST

Forget this. I see how it was a "vmd plotting" issue not physics...

On Thu, Dec 20, 2012 at 11:03 AM, Dr. Eddie <> wrote:

> Hi all,
> I using namd to run a solvated protein in a box with PBC. During the runs
> my protein tends to leave the box. I understand that it is still solvated,
> but it appears it is not explicitly solvated.
> When I (using vmd) look at the Hbonds between some side chains' oxygen and
> water I get different behavior when the protein is inside the actual box
> vs when it is outside. When it is inside the actual box it will make
> explicit Hbonds with the water. Once outside the box it will never do that.
> I understand this to mean that while the protein is outside the actual box
> (and wrap water is on) the protein interacts with the image o the water but
> can't form an actual Hbond with the image.
> If I use wrap all then the protein will eventually come back but it will
> spend time with some of it outside the box (before enough of it is outside
> to wrap) and experience the same lack of Hbond intermittently.
> Has anyone else had this sort of issue and come to a resolution? I know I
> can use collective variables to keep the protein in the center of the box,
> but I worry that may also change the behavior of the protein. Clearly a
> much larger box is not realistic, although ideal.
> Thanks in advance for the help!!
> Eddie


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