[gmx-users] Re: Re:Max diversity calculation

[Anton Feenstra]

Alexander wrote:
> Thank you Marc,
> 
> 
>>May be you can try to construct a block RMSD matrix (all against all)
>>(g_mdmat), cluster it (g_cluster), and select a representative for each
>>cluster
> 
> 
> But in this case we ignore the structures outside the clusters, where diversity is
> very high :(.
> 
> Thank you Anton,
> 
> 
>>Or, simply find the highest value in the matrix, and get the corresponding
>>pair of structures (use trjconv -s -f -dump <time> -o <time>.pdb).
> 
> 
> But what can I do if I need 5-10 structures with maximal RMSD in
> this small multitude?

You could simply select the 3-5 spots with highest RMS values in the matrix,
which would correspond to 4-10 structures (3 spots correspond to at least 4
structures, 5 spots to at most 10).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
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|  _   _  ___,| K. Anton Feenstra                                     |
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