[gmx-users] Re:g_clustsize problem

[Wang Zhun]

Hi, David,
The command I use is
g_cluster -f traj.trr -s topol.tpr -cutoff 0.2 -minstruct 2 -o rmsd-clust.xpm -g cluster.log 
 choose group 1  Protein
and
g_clustsize -f traj.trr -o csize.xpm -cut 0.2  -n index.ndx
 choose group 1  Protein
the following is part of cluster log which says 12 clusters found rather than 1 cluster:
Using linkage method for clustering
Using RMSD cutoff 0.2 nm
The RMSD ranges from 0.0738896 to 2.25219 nm
Average RMSD is 0.61356
Number of structures for matrix 4001
Energy of the matrix is 1004.6 nm

Found 12 clusters


cl. | #st rmsd | middle rmsd | cluster members
  1 |   1      |      0      |      0
  2 |   8 .612 |      5 .271 |      5     10     15     20     25     30     35
    |          |             |     40
  3 |   21.084 |     45 .169 |     45     50
  4 |  141.636 |     55 .292 |     55     60     65     70     75     80     85
    |          |             |     90     95    100    105    110    115    120
  5 |   32.092 |    125 .197 |    125    130    135
  6 |  132.640 |    140 .292 |    140    145    150    155    160    165    170
    |          |             |    175    180    185    190    195    200
  7 |  313.199 |    205 .433 |    205    210    215    220    225    230    235
    |          |             |    240    245    250    255    260    265    270
    |          |             |    275    280    285    290    295    300    305
    |          |             |    310    315    320    325    330    335    340
    |          |             |    345    350    355
  8 |   23.572 |    360 .143 |    360    365
  9 |   74.119 |    370 .264 |    370    375    380    385    390    395    400
 10 |  124.633 |    405 .283 |    405    410    415    420    425    430    435
    |          |             |    440    445    450    455    460
 11 |  325.164 |    465 .356 |    465    470    475    480    485    490    495
    |          |             |    500    505    510    515    520    525    530
    |          |             |    535    540    545    550    555    560    565
    |          |             |    570    575    580    585    590    595    600
    |          |             |    605    610    615    620
 12 | 38765.784 |    810 .806 |    625    630    635    640    645    650    655
    |          |             |    660    665    670    675    680    685    690
    |          |             |    695    700    705    710    715    720    725
    |          |             |    730    735    740    745    750    755    760
    |          |             |    765    770    775    780    785    790    795
    |          |             |    800    805    810    815    820    825    830
    |          |             |    835    840    845    850    855    860    865
    |          |             |    870    875    880    885    890    895    900
    |          |             |    905    910    915    920    925    930    935
    |          |             |    940    945    950    955    960    965    970
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