[gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 15 14:26:00 CET 2008

> Hi all,
> I have two questions about the g_cluster.
> 1)
> I want to test the performance of the clustering methods implemented in g_cluster. However, although there are some information about the gromos,Jarvis Patrick, and single linkage methods both in the manual and on the internet, there are no information about the implementation of both the Monte Carlo and the diagonalization method. 
> I know that when diagonalizing a matrix, the eigenvalues are found, and then how they are used for the clustering? 
use the source. this is not a published or very well tested method. so 
please be careful when using it.

> 2)There are two options for the -dista option of the g_cluster: rmsd of distance and RMS deviation. What is the difference between these two?
> One of them gives the absolute rmsd of each frame and the other gives the relative rmsd according to the average rmsd?
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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