Thanks so much Sir.
What was the cluster population? The cluster population was 1.
How many clusters did you obtain? I obtained 1 cluster only.
Did the cluster pop. vs time plots look OK for them? Yes it showed one
horizontal straight line.
Did you look at how many frames were clustered vs how many noise frames you
obtained. There are 20000 frames clustered and no noise frame.
Did you look at any clustering metrics like DBI, pseudo F, etc? I do not so
understand it.
Did you try to optimize your input parameters for the DBScan algorithm
using K-dist plots as described in the manual? Not yes Sir, where is
the manual.
Thanks.
nadaafiva
Pada tanggal Rab, 24 Jun 2020 pukul 19.16 Daniel Roe <daniel.r.roe.gmail.com>
menulis:
> Hi,
>
> We need more information. What was the cluster population? Were the
> rest of your clustering results reasonable? How many clusters did you
> obtain? Did the cluster pop. vs time plots look OK for them? Did you
> look at how many frames were clustered vs how many noise frames you
> obtained? Did you look at any clustering metrics like DBI, pseudo F,
> etc? Did you try to optimize your input parameters for the DBScan
> algorithm using K-dist plots as described in the manual?
>
> It would also help if you stated the version of cpptraj you are using.
>
> -Dan
>
> On Sat, Jun 20, 2020 at 4:58 AM Nada Afiva <nadaafiva.gmail.com> wrote:
> >
> > Dear Amber,
> > I performed a cluster analysis using the input below.
> > However, I got a strange result in which the file
> > "cluster-cpopvtime-x1d1.agr"
> > show one straight line only.
> > Hope you can help me.
> > Thank you in advance.
> >
> > Best,
> > nadaafiva
> >
> >
> > Here is my input file
> > # Cluster analysis with cpptraj.
> >
> > parm x1d1.prmtop
> > trajin nowat.prod.nc
> >
> > cluster C0 \
> > dbscan minpoints 25 epsilon 0.9 sievetoframe \
> > rms :1-1079.CA \
> > sieve 10 \
> > out cluster-x1d1.dat \
> > summary cluster-summary-x1d1.dat \
> > info cluster-info-x1d1.dat \
> > cpopvtime cluster-cpopvtime-x1d1.agr normframe \
> > repout rep-cluster-x1d1 repfmt pdb \
> > singlerepout cluster-x1d1.nc singlerepfmt netcdf \
> > avgout cluster-avg-x1d1 avgfmt restart
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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Received on Thu Jun 25 2020 - 02:00:03 PDT
