[gmx-users] calculating com-com distances.

[Fernando C]

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
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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