[gmx-users] Steps for executing Markov state Modelling (MSM) analysis

Soham Sarkar soham9038 at gmail.com
Wed Mar 13 07:03:11 CET 2019

Dear all,
       I have a protein trajectory in xtc format. I want to do the MSM
analysis on this trajectory to see how the process is going on and the
meta-stable states. I have followed the Video series by Frank Noe and team
on MSM, but it is not clear to me how to start it. I have some questions,
1) What are the python packages that I need to install?
2) How should I start it?
3) What kind of data they have generated?
Any one with the introductory steps of MSM analysis, any link or hand-on
tutorial video is highly appreciated.
- Soham

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