<div dir="ltr">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:<br><br>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?<br>
<br>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)?<br>
<br>Many thanks!</div>