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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