Re: [AMBER] Population analysis

From: Jason Swails <>
Date: Mon, 15 Jun 2015 07:25:08 -0600

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
Received on Mon Jun 15 2015 - 06:30:05 PDT
Custom Search