[gmx-users] Regarding g_cluster output.

[Abhi Acharya]

Hello Gromacs users.

I ran g_clustsize on a trajectory file. The output gives the cluster
members in the last column. I don't understand, how these members are
numbered. My trajectory contains 25001 frames whereas the members are
numbered till 50000. The output I get is as follows:

Using gromos method for clustering
Using RMSD cutoff 0.1 nm
The RMSD ranges from 0.0398338 to 1.58 nm
Average RMSD is 0.10737
Number of structures for matrix 25001
Energy of the matrix is 6578.78 nm

Found 2519 clusters

Writing average structure for each cluster to clusters.pdb
Writing all structures for the first 20 clusters with more than 1
structures to clusters.pdb%04d.pdb
Counted 7269 transitions in total, max 19 between two specific clusters

cl. | #st  rmsd | middle rmsd | cluster members
  1 | 575  0.106 |  44164 .087 |  39816  39988  40246  41958  41960  41968
 42266
    |           |             |  42290  42292  42294  42340  42342  42346
 42352
    |           |             |  42358  42360  42362  42364  42366  42410
 42412
    |           |             |  42414  42416  42418  42420  42422  42424
 42426
    |           |             |  42432  42434  42436  42438  42440  42442
 42444
    |           |             |  42452  42454  42456  42458  42460  42462
 42478
    |           |             |  42490  42492  42494  42534  42542  42560
 42572
    |           |             |  42620  42730  42878  42880  42900  42902
 42908
    |           |             |  42912  42914  42964  42966  42968  42970
 42972
    |           |             |  42974  42976  42978  42980  42982  42984
 42990


Thanks in advance.

Regards,
Abhishek Acharya
Shasara Research Foundation