[gmx-users] clusters of conformations of a molecular structure using g_cluster

段宝根 duanbg at sioc.ac.cn
Thu Nov 18 01:29:22 CET 2010

Hi, gmx-users

    I want to know whether the g_cluster is appropriate to analyze clusters of conformations of a structure from a trajectory, and how to use it correctly to attain the right results? 
    I try to analyze the clusters of conformations of a structure using g_cluster. But the output *.pdb clusters file seemed not to be right.
    g_cluster -f *.xtc -s *.tpr -wcl 10 -cutoff 0.1 -method -linkage; the only 1 cluster was found. And the results are different when I add the option -    fit or -nofit.  The explanation of manual to the option -fit is using least squares fitting before RMSD calculation. what is the meaning about it in detail?
Thanks for great help.

Yours Sincerely

Duan baogen
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