[gmx-users] Axis of the box in Gromacs

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 25 22:13:25 CEST 2013

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


On Thu, Jul 25, 2013 at 9:56 PM, Neha <nshafique at 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?
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