Re: Behavior of explicit water beyond periodic boundaries

From: Aron Broom (
Date: Thu Dec 20 2012 - 11:56:30 CST

oh ok, nvm also then.

On Thu, Dec 20, 2012 at 12:56 PM, Aron Broom <> wrote:

> 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.
> ~Aron
> 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

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:23 CST