[gmx-users] Transition matrix generation

[pratibha kapoor]

Hi,

I have done MD simulations on my system and have generated clusters of my
interest. Now, I would like to look at the transitions between different
clusters and henceforth the most probable pathway.
Is there any inbuild software that can do this?
I have read some of the papers which have analyzed using markov state model
followed by transition path sampling. Any idea how all these can be done
using some inbuild scripts?

Thanks