[gmx-users] clustering dynamical structures

Dmitri Dubov ddubov at ngs.ru
Wed Aug 19 06:07:46 CEST 2009

Dear GMX'ers,

Many gmx tools (g_rms, g_rmsdist, g_cluster etc.) calculate RMSD of distances. Take some molecule having two docking sites (A and B) and hydrated with two water molecules (C and D). Let's inspect two structures realized. The first structure is with C docking to A and D to B, and the 2nd one has C docking to B and D to A. These structures have large RMSD of distances between FIXED PAIRS OF  THEIR ATOMS, and to my knowledge g_cluster will differ them. How can I cluster these structures?

(Actually it is a very simplified example of my problem. My need is in clustering structures for system with many permutations.)
уBest regards,
 Dmitri                          mailto:ddubov at ngs.ru
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