[gmx-users] Axis of the box in Gromacs

Neha nshafique at wesleyan.edu
Thu Jul 25 21:56:08 CEST 2013

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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