[gmx-users] nstxout and cluster

[David van der Spoel]

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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you can have the analysis tool use only every Nth step. Use the -h flag.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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