[gmx-users] g_cluster warning message

simon sham ssham44 at yahoo.com
Thu Apr 7 19:07:37 CEST 2011

I have been trying to generate a pdb file using g_cluster with the following command:
"g_cluster -s md.tpr -f md.xtc -cl"

It ran O.K. but I am curious the rmsd warning message:
The RMSD ranges from 0.0481586 to 0.200779 nm
Average RMSD is 0.124039
Number of structures for matrix 5001
Energy of the matrix is 204.264 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0481586
Linking structures **
Sorting and renumbering clusters

What is that rmsd minimum 0 all about?

Thanks for your help in advance.

Simon Sham
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