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
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Received on Wed Jun 24 2020 - 05:30:04 PDT
