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
> > >> _______________________________________________
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> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
> >
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Received on Tue Jan 14 2020 - 10:00:02 PST
