[gmx-users] clustering dynamical structures

Dmitri Dubov ddubov at ngs.ru
Wed Aug 19 08:53:35 CEST 2009

Mark wrote:

> Dmitri Dubov wrote:
>> 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?

> You should test your hypothesis with g_cluster by converting two such 
> frames to a .pdb "trajectory" with trjconv, and then editing by hand to
> permute such a pair, and comparing the results before and after permutation.

- Yes, I sure have done it: g_rms calculates nonzero RMSD of distances between initial and permuted structure.

>> (Actually it is a very simplified example of my problem. My need is in clustering structures for system with many permutations.)

> It's hard to advise when we don't know your real objective. Do you want
> to cluster over fully solvated structures, but losing fixed-pair mapping
> of waters? If so, then that's going to require quite expensive 
> permutation over all possible orders of waters to find the global 
> minimum RMSD. Heuristics exist to find a close-to-minimum permutation,
> but guaranteeing global minima is hard.

> On the other hand, if you merely want to cluster with any waters in the
> docking sites permuted, and ignore the rest, then you may need to script
> g_dist using each water molecule as a group and a key atom in a docking
> site as a group in order to identify the water molecule(s) in the site.
> Then trjconv with the same index file and that info can write a 
> trajectory with just the selected waters. Now you may merely need to 
> permute over a handful of possibilities with g_rms, before finally 
> writing the permuted selected waters + solute to a trajectory (with 
> trjconv). This is now prepared for clustering with g_cluster - the 
> waters are ordered such that fixed-pair mapping makes sense.

Thanks for your advice! g_dist + trjconv may be helpful...

> Mark
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