[gmx-users] cannot output all the structures of one cluster

Zhenyu Meng fdmm1989 at gmail.com
Tue Jun 7 06:20:42 CEST 2016


Dear GMX users,
I want to output all the structures of certain cluster using g_cluster, and
the following is my command:
g_cluster -f md5_mol.xtc -s md5.tpr -n index.ndx -o md5.xpm -g
md5_cluster.log -cutoff 0.12 -cl cluster1.gro -wcl 1 -nst 30
While it seems gromacs cannot generate all the structures. Instead, in
cluster1.gro there're only several central structures.
The .log file is like this:
Writing middle structure for each cluster to cluster1.gro
Writing all structures for the first 1 clusters with more than 30
structures to cluster1.gro%01d.gro
But I cannot find cluster1.gro%01d.gro in my directory.
Is there anyone knowing what's going on?
Your help will be highly appreciated!

-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University


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