Dear Giacomo, You can use the -dt flag in g_cluster.
Ran. 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ------------------------------------------------------ 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
