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

[Mark Abraham]

Hi,

You don't want periodic imaging to affect which z coordinates are in which
bin, so you want a large range of z

Mark

On Wed, Jul 25, 2018, 09:42 Alex <alexanderwien2k at gmail.com> wrote:

> 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
> > > --
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