[gmx-users] rules of thumb to select a cutoff for clustering

Thomas Evangelidis tevang3 at gmail.com
Fri Jan 27 13:31:13 CET 2012

I know that this topic has been mentioned again in the mailing list, yet no
explicit answer has been given. So my questions are:

1. How can I utilize the output files of g_cluster (rms-distribution.xvg,
cluster-sizes.xvg, cluster-id-over-time.xvg, cluster-transitions* ) to
decide which is the best cutoff to use with the gromos algorithm for my

2. What do these warning messages mean and how can I use them for the
cutoff decision?

WARNING: rmsd cutoff 1.2 is outside range of rmsd values 0.0283 to 0.559
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0283

I would greatly appreciate any advice!




Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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