Thank you very much for your answers. However I think I did not express
correctly. My question goes in another sense.
For what I know, cluster plots usually start at the maximum of the y axis
(1), meaning all conformations belong to the same cluster until the moment
where another cluster is found; where the first starts to decrease as the
second increases, and so on.
In my case, pop1 starts at the bottom of the y axis and rapidly increases,
without reaching the unit. Then everything is as expected. But what I don't
understand is why dbscan does not assume the 100% of the data as part of
the first cluster. Where does that difference come from?
Is this behaviour normal?
Hope I explained better this time.
Thank you again,
El jue., 13 jun. 2019 21:50, Daniel Roe <daniel.r.roe.gmail.com> escribió:
> On Thu, Jun 13, 2019 at 3:45 PM Thomas Cheatham <tec3.utah.edu> wrote:
> >
> > Perhaps my fault, C programmer... Easy fix +1 or convert to FORTRAN
>
> Ha, never! I wish everything started from 0...
>
> >
> > > On Jun 13, 2019, at 9:12 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > >
> > > Hi,
> > >
> > > Historically, PTRAJ always numbered clusters starting from 0 and
> > > sorted by population (cluster 0 = most populated). CPPTRAJ has
> > > continued this convention. All cluster output should have a cluster 0.
> > >
> > > -Dan
> > >
> > >> On Thu, Jun 13, 2019 at 1:04 PM <dnlfr1994.gmail.com> wrote:
> > >>
> > >> Dear users,
> > >>
> > >>
> > >>
> > >> I am currently working on clustering analysis of several MD with a
> system
> > >> with 600 aminoacids for 200 ns simulations.
> > >>
> > >> I have plotted the kdist plots for kdist 1 to 10 and from this results
> > >> obtained I use the following input:
> > >>
> > >>
> > >>
> > >> cluster C0 dbscan minpoints 4 epsilon 1 sievetoframe rms :1-279 sieve
> 10 \
> > >>
> > >> out dbscan_clust/cnumvtime.dat sil Sil \
> > >>
> > >> summary dbscan_clust/summary.dat info dbscan_clust/info.dat \
> > >>
> > >> cpopvtime dbscan_clust/cpopvtime.agr normframe repout
> > >> dbscan_clust/rep repfmt pdb \
> > >>
> > >> singlerepout dbscan_clust/singlerep.nc singlerepfmt netcdf
> avgout
> > >> Avg avgfmt restart
> > >>
> > >> run
> > >>
> > >> clear all
> > >>
> > >>
> > >>
> > >> The clustering runs OK with no noticeable problems. However, it has me
> > >> intrigued to see that unlike all other clustering plots I have seen
> > >> (clusters starting at 1), the clusters on this one start from cero. I
> fail
> > >> to find a reason for this behaviour. Find a picture of the pop vs
> frame I
> > >> get at the bottom of this message.
> > >>
> > >>
> > >>
> > >> I would really appreciate it if anyone could help me solve this
> problem
> > >>
> > >>
> > >>
> > >> Thank you in advance,
> > >>
> > >>
> > >>
> > >> Daniel Fernández
> > >>
> > >>
> > >>
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Received on Thu Jun 13 2019 - 15:30:03 PDT
