Dear Caterina, GMX users, Whether or not the various clusters really represented different conformational states depends on your system and on the definition of the clusters (and of the conformational state). You can have some idea about the difference between the clusters by examining the central structures. However, a single measure (e. g. clustering analysis) is generally not enough to gain structural insights in complex structures such as proteins.
The same is true for stability. The fact that you have transitions cannot state whether or not the simulation is stable (unless you simulate only for a short time). You may want to check other parameters such as the overall and matrix rmsd, secondary structure, energy component etc. to see if the simulation is stable. Examining the trajectory can also help. Hope it helped, Ran. Caterina Arcangeli wrote: > 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 > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
