Subject: clustering of a huge number of conformations

From: Robert Gdanitz <[email-masked]>
Date: Mon, 10 May 1999 21:06:09 +0200 (MET DST)

In the special case that N molecular conformations are to be clustered into M
sets in order to obtain low-energy structures, one may use an algorithm that
needs roughly N x M steps. Provided that M is not too large, the algorithm thus
can also be used for large N.

The algorithm proceeds as follows: i) look for the conformation which is lowest
in energy (N step); ii) compare this conformation with all the others and join
similar ones to the cluster (N step); iii) delete the cluster from the original
set of yet unclustered conformation (bookkeeping); iv) repeat these steps M 
times.

I have used this algorithm to cluster low-energy molecular crystal structures
generated by Monte-Carlo simulated annealing, see: Chem. Phys. Lett. 190 (1992)
391.
-- 
PDr. Robert J. Gdanitz         Institut f. Physikalische u. Theoretische Chemie
Phone: +49 531 391-5370        Technische Universitaet, Hans-Sommer-Str. 10
Fax:   +49 531 391-5396        D-38106 Braunschweig, Germany
email: [email-masked]        http://www.tu-bs.de/~gdanitz