Thanks a lot Daniel, it works.
On Mon, Jun 15, 2015 at 6:21 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> (801) 585-6208 (Fax)
> _______________________________________________
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> 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
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Received on Mon Jun 15 2015 - 09:00:02 PDT
