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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
