If the box is periodic, then it is everywhere. mdrun makes no promises
about its output being mapped to a particular box.

Mark

On Thu, Jul 25, 2013 at 9:56 PM, Neha <nshafi...@wesleyan.edu> wrote:
> Hi everybody,
>
> I was wondering if you could answer a quick question I had. Where does the
> axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of
> the box, but if that was true none of the x, y, z values for position should
> be negative. However in my trajectory I see a value with a negative sign
> before it which implies the axis might be somewhere else. It seems to happen
> pretty rarely, so I am not sure why a) more of the values are not in the
> negative direction or b) why that would happen in this one particular case?
>
>
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Axis-of-the-box-in-Gromacs-tp5010131.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to