[gmx-users] g_cluster nan/segmentation fault error

[mahealey]

Hi All,

I'm trying to cluster a pdb trajectory format file and I'm getting odd
results.  The command line i'm using is:

g_cluster -f 0to7.pdb -s cysTerm.pdb -g cluster.log -o rmsd-clust.xpm -dist
rmsd-dist.xvg -cl clusters.pdb -method monte-carlo -seed 4540 -niter 10000


And everything seems to go fine until the end, where it spits out the
following set of results (input for fitting is C-Alpha, output C-Alpha):

Reading frame       0 time   -1.000    '', 2038 atoms
Reading frame    1600 time 1599.000   
Allocated 41086080 bytes for frames
Read 1680 frames from trajectory 0to7.pdb
Computing 1680x1680 RMS deviation matrix
# RMSD calculations left: 0         

The RMSD ranges from -nan to -nan nm
Average RMSD is -nan
Number of structures for matrix 1680
Energy of the matrix is -nan nm
Segmentation fault


I don't honestly understand whats going on here, does anybody else have any
ideas?

Mark

Ps.  I'm pretty new to using the clustering utility.




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