marscher
commented
5 years ago Dear Tanmoy,
you should use dtrajs_active, which are restricted to the active set (e.g. largest connected set of states in all of your trajectories), to perform the mapping to metastable_assignments.
Kind regards, Martin
Dear pyEMMA users, It's Tanmoy from IIT Kharagpur, India. I was trying the MSM. But I am having some problem while executing PCCA+. While executing :
Cluster into macrostate
nstates = 2 msm.pcca(nstates) metastable_traj = msm.metastable_assignments[dtrajs_concatenated]
I am having the following error
index 198 is out of bounds for axis 0 with size 196
It is coming due numpy array miss match, I guess. But I don't know how to fix this. Can you please help. I have attached the file with this mail.
regard Tanmoy