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<DIV>Hi, gmx-users</DIV>
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<DIV> 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? </DIV>
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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.</DIV>
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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?</DIV>
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<DIV>Thanks for great help.</DIV>
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<DIV>Yours Sincerely</DIV>
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<DIV>Duan baogen</DIV></FONT></DIV>
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