[gmx-users] cluster analysis of flexible peptide trajectory

Thomas Evangelidis tevang3 at gmail.com
Fri Mar 16 16:03:55 CET 2012

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

Thanks in advance,
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