[gmx-users] Re: Re:Max diversity calculation
feenstra at chem.vu.nl
Tue May 20 14:56:02 CEST 2003
> 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
> 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).
| | |
| _ _ ___,| K. Anton Feenstra |
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