Re: [AMBER] Population analysis

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Mon, 15 Jun 2015 17:51:11 +0300

Hi Jason and Parker,

Thanks for your suggestions. Following Jason's suggestion, I generated
three distance data sets and did as follows:

trajin ../SB-cpdI-prod.binpos

distance omega3 @7368 @7480
distance omega2 .7369 @7480
distance omega1 @7370 @7480

hist omega3,*,*,*,20 omega2,*,*,*,20 omega1,*,*,*,20 out hist.gnu

go

and I got hist.gnu as output file which has four columns omega3,2,1 and
Hist_003. However, I am unable to interpret the output of hist.gnu. It
seems to me that first three columns are the distances with time series but
what is the significance of fourth column i.e. hist_003? Please help me to
interpret the histogram output.

Regards
kshatresh

On Mon, Jun 15, 2015 at 4:39 PM, Parker de Waal <Parker.deWaal.vai.org>
wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 15 2015 - 08:00:03 PDT
Custom Search