[gmx-users] Re: question about non-orthongonal box vectors in pdc

[Tsjerk Wassenaar]

Hi Michael,

It will in any case still fill up space in a periodic way. That can be done
with an infinite number of triclinic boxes, of which the formal (perfectly
regular) truncated octahedron is only one. Besides, the shift vectors are
used to calculate the distances between particles, determine the neighbour
lists, etc. If the coordinates are only stored with a certain precision,
there is no point in having lattice vectors (box vectors) available with
higher precision. You may want to read a bit on periodic boundary conditions
from Henk Bekker (notably his 1996 JCC paper).

By the way.., don't use the truncated octahedron (unless it's for
comparison), try a rhombic dodecahedron instead. It's smaller and most
likely better in terms of the simulation results.

Cheers,

Tsjerk

On 3/30/06, Michael Shirts <mrshirts at gmail.com> wrote:
>
> That would be pbc (periodic boundary conditions), not pdc (who knows
> what that is), of course . . .
>
> On 3/30/06, Michael Shirts <mrshirts at gmail.com> wrote:
> > So, to get a truncated octahedron, or some other shape, you use
> > certain ratios for the box vectors as detailed in the manual.  But the
> > box vectors in the .gro file are truncated to a certain precision, so
> > don't exactly meet these ratios.  What is the consequence of not
> > exactly meeting these ratios?  It won't precisely fill space in a
> > periodic way -- so does it mess up the pbc in some way?  Anyone know?
> >  Any experiences?  Should I make sure the ratios are correct up to
> > machine precision?  Is there a way to handle this more robustly?
> >
> > Thanks,
> > Michael Shirts
> > Research Fellow
> > Columbia University
> >
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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