Re: Behavior of explicit water beyond periodic boundaries

From: Aron Broom (
Date: Thu Dec 20 2012 - 11:56:11 CST

I'm not clear on why you think it's not forming H-bonds with the water
images? Obviously if you're calling H-bonds anything where you can measure
that distance, and you're only counting the single periodic image, you
won't detect those H-bonds, but if you either recenter the periodic cell
around the protein (forget how this is done in VMD) or replicate the cell,
you should be able to detect them again no?

Maybe I'm not getting it.


On Thu, Dec 20, 2012 at 12:03 PM, 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

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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