# [gmx-users] calculating com-com distances.

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 14 20:29:12 CEST 2009

Hi Fernando,

Just bear in mind that these lattice vectors are just translation
vectors. You can add them to or subtract them from the positional
vectors of the com. That way you'll get a number of points which you
can use to calculate the distances the regular way. To see where you
went wrong, consider that a vector of the triclinic unit cell may have
more than one non-zero component. You considered only one non-zero
component, based upon the rectangular brick representation. But from
Pythagoras theorem it follows that doing so will make you miss part of
the true distance and come to an underestimate of it.
There is a niftier solution to the smallest distance, which will work
regardless of the separation between particles/coms in the infinite
system. It's in my thesis (Chapter 3, Appendix C, page 68):
http://dissertations.ub.rug.nl/faculties/science/2006/t.a.wassenaar/?FullItemRecord=ON

Hope it helps,

Tsjerk

On 4/14/09, Fernando C <fernando.cesar.lf at gmail.com> wrote:
> Hi Tsjerk and all list!
>
>  > You have to use the three vectors from the tricilinic representation
>  > to obtain the correct distance in the periodic system. Check PBC in
>  > Chapter 3 of the manual.
>
>
>  I used the length values from rectangular box because I'd want believe that
> my problem would be solved easily; I wouldn't want to fall in question of
> calculate positions and distances in triclinic cells. But here I am: could
> anybody explain to me the algorithm of how such things are calculated?
>
>  Thanks again!
>
>  Fernando.
>
>
>
>
>
>  --
>  And Noel Gallagher said: Gromacs is gonna live forever!
>
> 2009/4/13 Tsjerk Wassenaar <tsjerkw at gmail.com>
> >
> > Hi Fernando,
> >
> >
> > > I've obtained the vectors for the rectangular box in g_energy,
> > > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the
> > > skewed box.)
> >
> > You have to use the three vectors from the tricilinic representation
> > to obtain the correct distance in the periodic system. Check PBC in
> > Chapter 3 of the manual.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University