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
>
>
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Received on Thu Jul 02 2020 - 06:00:04 PDT
