[gmx-users] Question about g_cluster

[Jacob Durrant]

I recently started using g_cluster and have a question. When I run
g_cluster, the program asks me to select two groups. The output looks
something like this:

Select group for least squares fit and RMSD calculation:
Group     0 (     C-alpha) has   383 elements
Group     1 ( active_site) has  2438 elements
Select a group: 0

Select group for output:
Group     0 (     C-alpha) has   383 elements
Group     1 ( active_site) has  2438 elements
Select a group: 1

I have assumed that g_cluster aligns the trajectory by the first group
selected, and then clusters based on the second group. Recently, however,
someone told me that both the alignment and the clustering is performed only
on the first group. Can anyone confirm this? If so, what's the purpose of
the second group?

Thanks,

Jacob
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