OK - I've been looking at this for a bit. I think that the problem
must be that all your points too close i.e. all points are within
epsilon from each other. Your dvdfile backs that up - the first column
is '#Density', which just means # of points that are within epsilon
from that point. In each case the #Density is 1249, indicating that
everyone is too tight. I think if you lower epsilon you'll start to
get better results.
This is probably a case that cpptraj should trap. In my (limited)
defense, it does state that the 'dpeaks' implementation is under
development...
So in summary, try lowering epsilon and see if that helps. I'll work
on an update to trap the case where epsilon is too large.
Hope this helps,
-Dan
On Tue, Jan 14, 2020 at 12:34 PM <yinglong.miao.gmail.com> wrote:
>
> I have also tried the gauss option. It gave the following output:
> ACTION OUTPUT:
>
> ANALYSIS: Performing 1 analyses:
> 0: [cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
> runavg.dat deltafile delta.dat sieve 200 gauss]
> Starting clustering.
> Mask [*] corresponds to 15 atoms.
> Estimated pair-wise matrix memory usage: > 3.123 MB
> Pair-wise matrix set up with sieve, 250000 frames, 1250 sieved frames.
> Calculating pair-wise distances.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
>
> No error message was given but also no further output ...
>
> Thanks,
> Yinglong
>
>
> On Tue, Jan 14, 2020 at 9:47 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Can you provide me (either in reply to this or off list) your entire
> > cpptraj output and the contents of dvdfile?
> >
> > This could happen with very sparse density I think, although its
> > difficult to say without exactly replicating. You could potentially
> > try the 'gauss' keyword for Gaussian density instead of discrete
> > density.
> >
> > -Dan
> >
> > On Mon, Jan 13, 2020 at 8:10 PM Yinglong Miao <yinglong.miao.gmail.com>
> > wrote:
> > >
> > > Hi Dan,
> > >
> > > It’s the latest version as in AMBER git repository.
> > >
> > > Thanks,
> > > Yinglong
> > >
> > >
> > > > On Jan 13, 2020, at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > > >
> > > > What version of cpptraj are you using?
> > > >
> > > > -Dan
> > > >
> > > > On Mon, Jan 13, 2020 at 6:51 PM <yinglong.miao.gmail.com> wrote:
> > > >>
> > > >> Hello,
> > > >>
> > > >> I tried to use the dpeaks algorithm for clustering with the following
> > > >> command:
> > > >> cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
> > > >> runavg.dat deltafile delta.dat sieve 200
> > > >>
> > > >> But keep getting the following output with error:
> > > >> ...
> > > >> Finding closest neighbor point with higher density for each point.
> > > >> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
> > > >> Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor
> > is -1.
> > > >> Segmentation fault (core dumped)
> > > >>
> > > >> I will appreciate any suggestions that would fix this ...
> > > >>
> > > >> Thanks,
> > > >> Yinglong
> > > >>
> > > >> Yinglong Miao, Ph.D.
> > > >> Assistant Professor
> > > >> Center for Computational Biology and
> > > >> Department of Molecular Biosciences
> > > >> University of Kansas
> > > >> http://miao.compbio.ku.edu
> > > >> _______________________________________________
> > > >> 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
> >
> > _______________________________________________
> > 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
Received on Fri Jan 17 2020 - 07:00:02 PST
