[gmx-users] Shifting in minimization

Mark Abraham mark.j.abraham at gmail.com
Fri May 25 11:30:38 CEST 2018


mdrun suits itself because there's no way to guess how to keep everybody
happy with the form of the output.

You shouldn't need to care, but if you want to put the center of the box
somewhere, editconf and trjconv do that.


On Thu, May 24, 2018 at 9:58 PM Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
> I have system containing a solid slab and water molecules on top of it in a
> rectangle box (   6.67350 , 6.96840, 8.68584). I do not know why the whole
> slab completely shift in the Y direction after minimization!? The shift
> approximately is equal to the Y-cell size (6.96840). It might not be
> critical issue due to presence of PBC, but at least is weird and not good
> looking. The pressures in XX, YY are similar in my knowledge. Would you
> please let me know I can find the reason and how to fix it?
> Thank you
> Alex
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