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
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