[gmx-users] g_cluster settings

[Marc Charendoff]

Hello,

     I am trying to perform a cluster analysis on a 4 ns trajectory (4000 frame 
trajectory), but I am not getting any more than 1 cluster until I get down to a 
cutoff of 0.05 nm. This seems like an awfully small number, so I checked my rmsd 
distribution and found that 44% of my rmsds are at 0.1 nm or greater. My 
distribution looks like the following:

RMS (nm) a.u. 
0 0 
0.00288719 0 
0.00577439 0 
0.00866158 0 
0.0115488 1 
0.014436 15 
0.0173232 218 
0.0202104 1280 
0.0230976 4477 
0.0259848 11274 
0.0288719 22180 
0.0317591 36380 
0.0346463 52780 
0.0375335 69542 
0.0404207 86568 
0.0433079 103148 
0.0461951 119844 
0.0490823 137284 
0.0519695 154406 
0.0548567 172063 
0.0577439 187809 
0.0606311 203305 
0.0635183 216294 
0.0664055 226732 
0.0692927 234868 
0.0721799 241167 
0.0750671 246867 
0.0779543 250484 
0.0808415 251606 
0.0837286 249638 
0.0866158 245941 
0.089503 239141 
0.0923902 233838 
0.0952774 226234 
0.0981646 218675 
0.101052 209554 
0.103939 201564 
0.106826 193361 
0.109713 184787 
0.112601 176838 
0.115488 169245 
0.118375 161271 
0.121262 153375 
0.124149 147370 
0.127037 140140 
0.129924 133571 
0.132811 126590 
0.135698 119388 
0.138585 113458 
0.141473 106930 
0.14436 99864 
0.147247 93893 
0.150134 87665 
0.153021 81892 
0.155909 76306 
0.158796 71032 
0.161683 66218 
0.16457 61435 
0.167457 56912 
0.170344 52483 
0.173232 48423 
0.176119 44437 
0.179006 40809 
0.181893 37334 
0.18478 34464 
0.187668 31373 
0.190555 28641 
0.193442 26543 
0.196329 23790 
0.199216 21807 
0.202104 19579 
0.204991 17522 
0.207878 15397 
0.210765 13529 
0.213652 11875 
0.21654 10151 
0.219427 8822 
0.222314 7457 
0.225201 6312 
0.228088 5232 
0.230976 4214 
0.233863 3492 
0.23675 2681 
0.239637 2135 
0.242524 1770 
0.245412 1360 
0.248299 1021 
0.251186 806 
0.254073 525 
0.25696 468 
0.259848 277 
0.262735 192 
0.265622 137 
0.268509 103 
0.271396 46 
0.274283 40 
0.277171 17 
0.280058 7 
0.282945 8 
0.285832 2 
0.288719 1 

And my command line is as follows:

g_cluster -f md.trr -s md.tpr -n index.ndx -sz clustersize1.xvg -clid 
clusterid1.xvg -cutoff .10   -cl clusters1.pdb -b 1 -e 4001

Is there anything I'm missing? 

Guidance appreciated.

Regards, Marc
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