[gmx-users] Clustering based on other parameters than RMSD

soumadwip ghosh soumadwipghosh at gmail.com
Fri Oct 27 07:49:36 CEST 2017

Hi all,

I have a trajectory of 300 ns for a membrane protein. I want to sample
native/non-native conformations and compare across various systems. My
question is can parameters like number/occupancy of hbonds or the time
evolution of helical residues (output from gmx do_dssp) be clusterized
using something like gmx cluster or something similar? As far as I
understand gmx cluster does RMSD/distance RMSD clustering based on a
predefined cut-off. I am trying to extract the number of accessible
microstates for a given system, extract the corresponding trajectories and
do some property analysis. This is to be done based on proportion of
native/non-native like states which may be related to assigning partially
denaturated state of the protein. I did cluster analysis on PCA but it
seems difficult to compare across different systems since they have
different principal components.

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