[gmx-users] Shifting in minimization

[Mark Abraham]

Hi,

Sure, that's what trjconv -pbc and -ur are used for. There's no way to ask
mdrun to automatically do the particular operation you want.

Mark

On Tue, May 29, 2018 at 3:21 PM Alex <alexanderwien2k at gmail.com> wrote:

> Hi Mark,
> Thanks.
> 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:
> https://drive.google.com/open?id=1TwkgpesJPfFUiqxhl9rXBU33dwWn-tyD
> Regards,
> Alex
>
> On Fri, May 25, 2018 at 5:30 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > 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.
> >
> > Mark
> >
> > 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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