Dear GROMACS users, Obviously RMSD-based clustering is not the best approach to find frequently visited conformations of flexible peptides. The other approach would be to used backbone dihedral angles to cluster the frames (i.e. with g_dih). There are also several articles in the literature describing more sophisticated clustering techniques used for MD trajectories of flexible peptides (e.g. spectral clustering), yet I haven't found any program that implements these methods to cluster the frames of a trajectory. Could anyone please recommend me a program for cluster analysis of peptide MD trajectories?
Thanks in advance, Thomas
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