Re: [AMBER-Developers] CPPTRAJ: dpeaks clustering

From: Yinglong Miao <yimiao.ucsd.edu> Date: Tue, 31 May 2016 12:44:46 -0700

----
parm protein.prmtop
trajin md-reimaged.nc
## RMSD
reference pro.pdb
rms reference out rmsd-clustering.dat
:5-27,42-62,80-101,122-144,167-189,210-230,245-264.CA
rmsd :278.*&!.H= reference nofit out rmsd-lig-clustering.dat
strip :1-277
cluster C0 \
        dpeaks epsilon 1 dvdfile density_vs_dist.dat choosepoints auto
distancecut 1.0 runavg runavg.dat deltafile delta.dat \
        rms :1.*&!.H= nofit \
        sieve 1 \
        out cnumvtime.dat \
        summary summary.dat \
        info info.dat \
        cpopvtime cpopvtime.agr normframe \
        repout rep repfmt pdb \
        singlerepout singlerep.nc singlerepfmt netcdf \
        avgout Avg avgfmt restart
go
----
Yinglong
On Tue, May 31, 2016 at 12:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, May 31, 2016 at 11:36 AM, Yinglong Miao <yinglong.miao.gmail.com>
> wrote:
> > This may be also a question on the Users mailing list, but as I try the
> > cpptraj density peaks (dpeaks) clustering (which is great!), I notice the
> > following warning regarding seiving frames:
> > ...
> >         Restoring sieved frames.
> > FIXME: Adding sieved frames not yet supported.
> >
> > I'm wondering whether this will be coded in the near future.
>
> Eventually, 'dpeaks' clustering is still under development and I don't
> have a time frame for when it will be complete. As is stated in the
> output, 'dpeaks' as currently implemented should be used with caution.
> You may want to try the DBSCAN method which also density based and is
> a little better tested.
>
> > Also is there
> > a limit on the data size for the clustering other than memory usage? The
> > workstation I'm running has ~64G memory, but the program exited in the
> > middle of matrix calculation (crashed?) even with apparently enough
> memory:
> >
> >     Estimated pair-wise matrix memory usage: > 16.587 GB
> >     Pair-wise matrix set up, 91068 frames
> >  0% 10% 20% 30% mkdir: cannot create directory
> > `cluster-dpeaks-e1-ncstep1-sieve1': File exists
>
> That doesn't look like a memory error to me. Can you provide your
> exact cpptraj input?
>
> -Dan
>
> >
> > Any suggestions will be appreciated,
> >
> > Yinglong
> >
> > Yinglong Miao, Ph.D.
> > Research Specialist I, Howard Hughes Medical Institute
> > Assistant Project Scientist, Department of Pharmacology
> > University of California, San Diego
> > Tel: 858-822-0255; Email: yimiao.ucsd.edu
> > http://mccammon.ucsd.edu/~ymiao/
> > http://gamd.ucsd.edu
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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> AMBER-Developers.ambermd.org
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>
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