[gmx-users] Question about g_cluster

[Mark Abraham]

Jacob Durrant wrote:
> 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?

I agree that "output" is ambiguous. g_cluster -h is also silent on both 
the need to provide these groups and what they're used for. Perhaps an 
improvement to the documentation is in order.

Mark