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

[Alexander]

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?

Best regards,

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
______________________________________________
E-mail: yakovenko_a at ukr.net