[gmx-users] g_cluster

[Nuno R. L. Ferreira]

> What about the .xpm file obatined with the -o flag? You have for each
> combination, a RMSD value. Search for the minimum in the x-pixmap ascii
> file. Ignoring the identity combinations (same structure I mean), search
the
> combinations which is assigned the "B" character. The "A" char means
RMSD=0.
>

After having written all this, I think that this approach doesn't lead you
anywhere. Simply because you could have a struture A with a tiny RMSD when
superimposed with struc. B, but when compared with struct. C, the RMSD has a
great value.
So, from the .xpm file you only get a distribution of the RMSD.