[gmx-users] g_cluster

Hendrik Preuss hendrik.preuss at chemie.uni-regensburg.de
Wed Feb 23 16:03:17 CET 2005

Dear gmx users,

some things are puzzling me with g_cluster:
1. In June 2004 Roman Affentranger wrote about a bug in g_cluster: The
cluster centers and the average RMSD values reported in the log-file are
incorrectly determined. My question is: Can I use g_cluster as it exists
or do I really have to change the source code to get appropriate
clusters with average/center structures?

2. Which cluster method would you recommend to gain useful structures
of a 2.5ns MD of a GPCR in a bilayer environment (full linkage, Jarvis
Patrick or gromos)?

Thanks a lot for your help,

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