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
Giacomo
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