Re: [AMBER] Population analysis

From: Parker de Waal <>
Date: Mon, 15 Jun 2015 13:39:44 +0000

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:

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,

From: Jason Swails []
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 <>

> 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
AMBER mailing list
Received on Mon Jun 15 2015 - 07:00:03 PDT
Custom Search