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

[OZGE ENGIN]

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? 

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
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Computational Science & Engineering
Koc University