Okay thanks so much for your explanations.
best regards,
nadaafiva
Pada tanggal Kam, 2 Jul 2020 pukul 19.48 David Cerutti <dscerutti.gmail.com>
menulis:
> One important thing to realize is that, if you stare down the axis of the
> truncated octahedron's triclinic representation, the obtuse angle you see
> is in fact 120 degrees, the acute angle 60 degrees. It is quite tilted
> indeed. For general triclinic boxes, yes you'll need to reassign the
> dimensions using ChBox. Make sure that the rest of your system is set up
> to tessellate and not clash when you do that!
>
> Dave
>
>
> On Thu, Jul 2, 2020 at 8:35 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Thu, Jul 02, 2020, Nada Afiva wrote:
> >
> > >I would like to use triclinic box shape for my system, but I am not sure
> > >how to assign it in tleap. If anyone knows, please helps.
> >
> > tleap doesn't know how to do this, aside from the special case of
> > solvating with a truncated octahedron, via SolvateBox. For a more
> > general case, use tleap's setBox command to create a periodic system,
> > then use the ChBox program (outside tleap) to enter the actual
> > dimensions you want.
> >
> > >Another question, is there any paper which compares truncated octahedron
> > and
> > >triclinic box shape?
> >
> > There are, but I can't seem to find the one I used to rely on now.
> > Check out the gromacs manual page, which may have the information you
> > want:
> >
> >
> >
> http://manual.gromacs.org/documentation/2019/reference-manual/algorithms/periodic-boundary-conditions.html
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 02 2020 - 18:00:03 PDT
