Hi,
Indeed I am getting noise frames. I think they come from a high rms change at the beginning of the simulation. Does it make sense? Are there any objections to a clustering graph like the one I have?
I am also getting negative silhouette values for pop 0 and 1, and low positive values for the others, what makes me think dbscan may not be the best algorithm for my system.
Any ideas on that?
Thank you very much
Daniel
-----Mensaje original-----
De: Daniel Roe <daniel.r.roe.gmail.com>
Enviado el: viernes, 14 de junio de 2019 15:46
Para: AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
Hi,
I see what you mean now. So without seeing your cluster data myself (something like your cluster population vs time data) I can't be certain, but I suspect you may be encountering "noise" frames, i.e.
frames that do not belong to any specific cluster. Could that be the case?
-Dan
On Thu, Jun 13, 2019 at 6:01 PM Daniel Fernández Remacha <dnlfr1994.gmail.com> wrote:
>
> 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 Mon Jun 17 2019 - 05:00:01 PDT
