Hi Kshatresh,
To overcome a similar problem I opted to build a simple markov chain to model residue distances states.
In my case I had one phosphoserine and proximal positively charged residues all of which were capable of forming a salt bridge.
To determine these interactions I used thed hbond calculation in CPPTRAJ and assigned markov states as follows:
http://192.95.24.46/markov.png
Using this, and my knowledge of which state persisted at the highest frequency I was able to determine the population frequencies and their exchange.
Hope this helps,
Parker
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Monday, June 15, 2015 9:25 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Population analysis
On Mon, Jun 15, 2015 at 1:54 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
> Dear Users,
>
> I want to calculate the population of distances of some atoms with
> specified atom during MD simulation, say, I have an atom X and I want to
> calculate the population of distances between X and C1, X and C2, X and C3
> in MD trajectories, here C1, C2, C3 are atoms closer to X.
> Is it possible to do with cluster command in cpptraj? I will be very
> thankful if someone can provide me an example to perform this calculation.
> I will be thankful to all suggestions.
>
​What you describe that you want is not clustering. It is essentially
histogramming the time series of distances. You *can* cluster on those
metrics if you want to, but clustering is not going to give you populations
of those distances.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 15 2015 - 07:00:03 PDT
