Hi,
The manual is the first link on this page: http://ambermd.org/GetAmber.php
There is a thorough section on clustering - look for the Analysis Commands
in Cpptraj.
To check the clustering metrics, you can look for the following (grep) in
the log file (assuming you have printed the cpptraj output to a log file):
DBI is Davies-Bouldon index
pSF is pseudo F
Number_of_noise_frames will give you how much of the trajectory frames is
classified as noise
What does the rms plot look like? Does it show a lot of motion? If the
system is restrained, it might be reasonable that you got a single cluster.
Alternatively, you can try using kmeans (or another distance-based
clustering algorithm) which will force a certain number of clusters.
I'd suggest starting with 3 or 5, saving the PairDistance file, and then
re-running the clustering with clusters=6,7,8,9,10 and the loadpairdist
command to see what the DBI/pSF metrics are.
Good luck!
-Christina
On Thu, Jun 25, 2020 at 4:32 AM Nada Afiva <nadaafiva.gmail.com> wrote:
> 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
> >
> > _______________________________________________
> > 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
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
-----------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 25 2020 - 06:30:04 PDT
