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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