Dear all,
A trajectory of umbrella sampling MD simulation for protein-peptide
complex separation (chains A and B) is ready with me.From visual
observation, i.e. extracted frames from the trajectory and aligned them
and make a movie along time, can view nice separation. However, I am
interested to perform cluster analysis over the trajectory to see
whether the biased translation of peptide follow some specific path or
not. The visual observation tells me that the translation happens in
steps. Therefore, I wish to check whether the cluster analysis also show
the same in term of more frame in clusters near these steps.
I am going through basic cluster command in CPPTRAJ, however, I am not
sure how to design.
I want to keep the chain A fixed and wish to see the clusters for
peptide chain B only.
Any input in this regard would be great help.
Thanking you in advance.
-- Josh
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Received on Wed Apr 05 2017 - 02:30:03 PDT
