[gmx-users] Shifting in minimization
alexanderwien2k at gmail.com
Tue May 29 15:21:26 CEST 2018
The problem is that only the slab shifts and water molecules stay x-y
centrally in the box. Similar to the picture in the link below:
On Fri, May 25, 2018 at 5:30 AM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > 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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