[gmx-users] distance options for g_cluster

Sun Feb 17 00:52:01 CET 2008

Hi all,

I am trying to understand what type of distance can be used with g_cluster? 

In the manual, it is written that  RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph. 
However, in the "other options" part, two options are indicated for 
-dista option, which indicates the type of distance that will be used with  g_cluster. They are RMSD of distances or RMS deviation. Consequently, the information in the "first paragraph" does not coincide with that given in the "other options" part for -dista option. 

Maybe I could not understand. Could anyone explain this in a clearer way, please?

Thanks in advance

Ozge Engin
Computational Science & Engineering
Koc University

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