[gmx-users] nstxout and cluster

Giacomo Bastianelli gbastian at pasteur.fr
Thu Nov 16 16:20:01 CET 2006

Dear Users,

after a 10ns of dynamics with a small protein (30 aa)
I tried to cluster the structure obtained from the trajectory.
this is the command I used:

g_cluster -f 1JJZ_10ns.xtc -s 1JJZ_10ns.tpr -o 1JJZ_rmsd_clust.xpm -g 
cluster.log -cutoff 0.1 -method linkage -rmsmin 1

I obtained a very huge matrix that take forever 50001x50001 to be solved...

Should I reduce the nstxout?
my setting is nstxout=5000 and each step is 0.002 ps.

Thanks in advance


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