[gmx-users] Re:g_clustsize problem

[David van der Spoel]

Wang Zhun wrote:
> 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
This is fine, results look OK. So what's the problem?

> and
> g_clustsize -f traj.trr -o csize.xpm -cut 0.2  -n index.ndx
>  choose group 1  Protein
This is not meaningful.

> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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