[gmx-users] Re: g_cluster rmsd definition (Roman Affentranger)

[Linda]

Thanks a lot, Roman,

     I will check and modify the code based on what you modified in your last mailinglist.

Greetings,

Linda

>>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 
>