Hello everyone, I am using g_cluster with gromos method to do some clustering, and by default, -cl writes the central structure of each cluster obtained.
So I wonder what 'central structure' mean? Assuming that I cluster based on RMSD values relative to the starting conformation, and that I then get a cluster with 3 structures (RMSD = 0.1, 0.2, 0.3 nm, respectively), should the structure with RMSD = 0.2 nm be the "central structure"? What if there are 4 structures in this cluster, with RMSD = 0.1, 0.2, 0.3, 0.4 nm, respectively? Thanks for any explanation, Yun
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