[gmx-users] g_cluster nan/segmentation fault error

mahealey mahealey at ualberta.ca
Mon Apr 1 00:43:02 CEST 2013

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


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

View this message in context: http://gromacs.5086.n6.nabble.com/g-cluster-nan-segmentation-fault-error-tp5006779.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list