[gmx-users] Steps for Markov State Modelling

[Justin Lemkul]

On 3/14/19 4:31 PM, Dallas Warren wrote:
> https://www.google.com/search?hl=&site=&q=MSM+analysis+%20Frank+Noe

Also relevant:

https://www.livecomsjournal.org/article/5965-introduction-to-markov-state-modeling-with-the-pyemma-software-article-v1-0

-Justin

> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Fri, 15 Mar 2019 at 06:57, Soham Sarkar <soham9038 at gmail.com> wrote:
>
>> 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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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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