[gmx-users] g_cluster rmsd definition

[Roman Affentranger]

At 15:15 24.06.2004 -0600, you wrote:
>Hi, all,
>
>         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?
>
>Thanks,
>
>Linda

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.

Regards

Roman