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

[Mark Abraham]

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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