[gmx-users] zig-zag stacking

[Lakshman Ji Verma]

Adding on to Dan’s suggestions, you can create a box containing two unit
cell using editconf (translate one molecule accordingly) and then replicate
that box using genconf to get required confirmation.

Thanks!
Lakshman

On Tue, Jul 31, 2018 at 6:39 PM Dan Gil <dan.gil9973 at gmail.com> wrote:

> Hi,
>
> I haven't tried it, but I wonder if the gmx editconf utility can be used to
> translate groups of atoms, where the group is defined with an index file
> (make_ndx).
>
> Dan
>
> On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati <
> nagasree.garapati at mail.wvu.edu> wrote:
>
> > Hi All
> >
> >
> > I am trying to look at the pore space availability and property
> > differences between supercells created by stacking unitcells on top of
> each
> > other and by zigzag stacking.
> >
> > In Gromacs genconf can be used to create a super cell by stacking unit
> > cells on top of each other, is there a way to create zig zag stacking?
> >
> >
> > Thank You
> >
> > With Regards
> > Nagasree Garapati
> > Research Assistant Professor
> > Dept of Chemical and Biomedical Engineering
> > West Virginia University
> > PO Box 6102
> > Morgantown, WV 26506-6102
> > 304 293-5028<tel:304%20293-5028>(O)
> > 304 276-3674(M)
> >
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