[gmx-users] Transition matrix generation

[Adelman, Joshua Lev]

On Jan 13, 2015, at 1:27 AM, pratibha kapoor wrote:

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

I'm not aware of any Markov State Modeling tools built directly into Gromacs, but there are several excellent third party tools. I've used MSMBuilder before and it will read gromacs trajectory files natively via MDTraj:
http://msmbuilder.org

There's also EMMA, which looks like it just takes the projection of your trajectory onto the state space:
http://pythonhosted.org/pyEMMA/

Hope that helps,
Josh