[gmx-users] g_cluster rmsd definition
roman.affentranger at bc.biol.ethz.ch
Fri Jun 25 08:59:13 CEST 2004
At 15:15 24.06.2004 -0600, you wrote:
> I would like to know the exact definition of two RMSDs in the
> cluster.log file.
>cl. | #st rmsd | middle rmsd | cluster members
> 1 | 1251 .221 | 6498 .109 | 6386 6474 6476 6478 ......
>i.e. does 0.221 stand for the biggest rmsd of a structure with the middle
>structre in cluster 1?
>does 0.109 stands for the rmsd between structure 6498 & original structure?
0.221 is the average RMSD of all pairs of cluster members.
0.109 is the average RMSD of all cluster members to the cluster center.
However, these values, together with the reported cluster center, will be
wrong unless you modified the code of gmx_cluster.c as suggested on the
mailing list two days ago.
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