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

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 25 08:17:08 CEST 2018


Maybe that's a limitation of gmx density. Make an equivalent .tpr with XYZ
periodicity and a sufficiently large z size.


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.

More information about the gromacs.org_gmx-users mailing list