[gmx-users] help on g_cluster transitions

[Caterina Arcangeli]

Hi all,
I'm doing cluster analysis of my protein simulation.
I use gromos method on the Ca atoms and I obtain 10 clusters.

Is not clear to me the (biological) meaning of transition between clusters.

1. Are transitions occurring among different conformational states?
2. What does means if one found several clusters-transitions: maybe that 
the simulation is not stable?

Thank to all.
Caterina


P.S.
Here is the .log file I've obtained:

------
Using gromos method for clustering
Using RMSD cutoff 0.1 nm
The RMSD ranges from 0.046404 to 0.181787 nm
Average RMSD is 0.117163
Number of structures for matrix 561
Energy of the matrix is 23.5304 nm

Found 10 clusters

Writing average structure for each cluster to 
cluster/pdb_average/F8M47_cluster.pdb
Writing all structures for clusters with more than 1 structures to 
cluster/pdb_average/F8M47_cluster%02d.pdb
Counted 106 transitions in total, max 17 between two specific clusters


cl. | #st rmsd | middle rmsd | cluster members
   1 | 264 .103 |   2832 .090 |   2302   2324   2370   2372   2374   2380
   2 | 128 .097 |   2082 .086 |   2020   2022   2024   2026   2028   2030
   3 |  49 .099 |   2368 .090 |   2262   2268   2274   2276   2282   2298
   4 |  48 .095 |   2650 .085 |   2514   2516   2518   2520   2526   2534
   5 |  34 .088 |   3086 .077 |   3028   3032   3040   3048   3050   3052
   6 |  18 .094 |   2260 .085 |   2232   2236   2238   2240   2242 2244 
    7 |  13 .092 |   2012 .081 |   2000   2002   2004   2006   2008 
2010     8 |   3 .090 |   2484 .086 |   2460   2484   2524
   9 |   3 .087 |   3110 .079 |   2914   3108   3110
  10 |   1      |   2332      |   2332