[gmx-users] a qiestion about using g_cluster

[Li Su]

Marcus Kubitzki writes: 

> Hi Li,
> first, generate an appropriate index file with make_ndx. There you can
> select the loops you want to analyze. Second, run g_cluster -s -f -n. 
> 
> Marcus 
> 
> Li Su wrote:
>> Dear Sir/Madam,
>> I am trying to use g_cluster to clusterize my protein trajectories. The 
>> proein core is very rigid, only loops will fluctuate. When I clusterize I 
>> want to clusterize only on the loops in stead of the whole protein. But 
>> when I use g_cluster it only offer choices on whole protein or c alpha or 
>> backbone and so on, all of which focus on the whole protein. I am 
>> wondering is there any way I can choose a part of the protein to 
>> clusterize? Thank you very much for your help! 
>> 
>> 
>> Best Wishes,
>> Li Su 
>> 
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> 
> -- 
> Marcus Kubitzki
> Max Planck Institute for Biophysical Chemistry
> Computational Biomolecular Dynamics Group
> Am Fassberg 11
> D-37077 Göttingen
> Germany
> phone: ++49-551-2012312
> fax: ++49-551-2012302
> Email: mkubitz[at]gwdg.de
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Dear Sir,
 Thank you so much for your kind help. But now I have another question. I 
think g_cluster will do a removing of translation and rotation displacement 
automatically. I am not quite sure whether it will do such part on the group 
of atoms I pick in the index file? If so is there any way I can specify 
which region to do the removement or if I can simply turn off the 
removement? I am asking this becuase what I really want to do is to fit all 
the snapshots by their cores and then clusterize the loop comformations. 
Even if I can just switch off the fitting, it will be good enough since I 
can use other routines to fit first. 


Best Wishes,
Li Su