[gmx-users] gromos analysis

[Wei Fu]

Hi, all,

    We converted the NAMD trajectory to gromacs format (from dcd to xtc
file), then use g_cluster
to analyze it, but it gives the imcomplete result in cluster.log as
follows:

Using gromos method for clustering
Using RMSD cutoff 0.1 nm
The RMSD ranges from 0.0701927 to 0.306038 nm
Average RMSD is 0.204764
Number of structures for matrix 1000
Energy of the matrix is 76.4664 nm

Found 83 clusters

_______________________________________________________________________
cl. | #st rmsd | middle rmsd | cluster members
  1 |  22 .201 |      0 .099 |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0
    |          |             |      0
  2 |  22 .196 |      0 .100 |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0
    |          |             |      0
  3 |  22 .192 |      0 .099 |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0
    |          |             |      0      0      0      0      0      0
0

... ...
_______________________________________________________________________

    I wonder why all cluster member is 0? 

    I also did the other analysis like rmsd, rmsf, and essential dynamics
analysis, all these commands work well. 

    Has anybody have idea about it? Thanks in advance!

Linda