[gmx-users] gmx density -d Z in a system with pbc = xy

[Alex]

Hi Mark,
Thanks.
You mean EITHER .tpr with XYZ periodicity OR a sufficiently large Z size
without periodicity in the Z direction?
Because with pbc = xyz doesn’t matter how large is the box in Z direction.
Regards,
Alex

On Wed, Jul 25, 2018 at 02:17 Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Maybe that's a limitation of gmx density. Make an equivalent .tpr with XYZ
> periodicity and a sufficiently large z size.
>
> Mark
>
> On Tue, Jul 24, 2018, 22:52 Alex <alexanderwien2k at gmail.com> wrote:
>
> > I have pbc only in X-Y directions in my simulations (pbc = xy), and I
> want
> > to calculate the number density in Z direction using the "gmx density -f
> > *.xtc -s *.tpr -d Z -dens number" but the gmx density just stuck in the
> > beginning. I wonder how I can density in Z direction in such situations?
> > Thank you.
> >
> > Best regards,
> > Alex
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>