[gmx-users] cluster analysis of flexible peptide trajectory

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

RE: [gmx-users] Cluster analysis

Sent: Friday, 9 March 2012 3:46 PM To: gmx-users@gromacs.org Subject: [gmx-users] Cluster analysis Hello, I would like to do cluster analysis in gromacs on my system which consists of a polymer and solvent . I would like to know how the solvent molecule surrounds around polymer and how many. Can

[gmx-users] Cluster analysis

Hello, I would like to do cluster analysis in gromacs on my system which consists of a polymer and solvent . I would like to know how the solvent molecule surrounds around polymer and how many. Can anybody help me out that how to start with or use g_cluster or g_clustsize in gromacs. Also there

[gmx-users] Cluster analysis

Dear all   Could you give me any suggestion about how I can interpretate output result of g_cluster? Is there a detailed tutorial?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at