Re: [AMBER] Population analysis

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 15 Jun 2015 07:25:08 -0600

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 15 2015 - 06:30:05 PDT
Custom Search