On Mon, Jun 15, 2015 at 8:51 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
>
> hist omega3,*,*,*,20 omega2,*,*,*,20 omega1,*,*,*,20 out hist.gnu
>
This is creating a 3D histogram from sets omega3, omega2, and omega1, and
probably should be output in a grid format (xplor or opendx). However, I
think what you wanted was a 1D histogram of each, for which you would use
the 'multihist' command:
multihist omega3 omega2 omega1 bins 20 out hist.agr
-Dan
>
> 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
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Jun 15 2015 - 08:30:02 PDT
