[gmx-users] nstxout and cluster

Ran Friedman r.friedman at bioc.unizh.ch
Thu Nov 16 16:33:06 CET 2006

Dear Giacomo,

You can use the -dt flag in g_cluster.


Giacomo Bastianelli wrote:
> 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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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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