[gmx-users] G_Cluster Questions

Anthony Ivetac aivetac at googlemail.com
Thu Oct 9 20:08:04 CEST 2008

I am using 'g_cluster' (-method gromos, version 3.3.1) to cluster the
conformations of a subset of residues in my protein from a MD trajectory and
have a couple of questions:

1. I have pre-fitted my trajectory on the 'core' of the protein and
therefore don't want g_cluster to refit my subset of residues for each RMSD
calculation, so I use the '-nofit' flag. However, when the program starts,
it asks me for an index group for "for least squares fit and RMSD
calculation". I assume this is a bug and it should be omitting the "least
squares fit" part?

2. In the output 'cluster.log' file, I see that the "Average RMSD is
0.124662". But when I open the 'rmsd-dist.xvg' output (the distribution of
RMSD values), the average RMSD (i.e. near the peak of the distribution) is
around 0.3 nm. Does the average printed in the 'cluster.log' file therefore
refer to some other average (i.e. not the average RMSD between all pairs of
structures in the trajectory)?

Many thanks!
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