On Thu, Jun 13, 2019 at 3:45 PM Thomas Cheatham <tec3.utah.edu> wrote:
>
> Perhaps my fault, C programmer... Easy fix +1 or convert to FORTRAN
Ha, never! I wish everything started from 0...
>
> > On Jun 13, 2019, at 9:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > Historically, PTRAJ always numbered clusters starting from 0 and
> > sorted by population (cluster 0 = most populated). CPPTRAJ has
> > continued this convention. All cluster output should have a cluster 0.
> >
> > -Dan
> >
> >> On Thu, Jun 13, 2019 at 1:04 PM <dnlfr1994.gmail.com> wrote:
> >>
> >> Dear users,
> >>
> >>
> >>
> >> I am currently working on clustering analysis of several MD with a system
> >> with 600 aminoacids for 200 ns simulations.
> >>
> >> I have plotted the kdist plots for kdist 1 to 10 and from this results
> >> obtained I use the following input:
> >>
> >>
> >>
> >> cluster C0 dbscan minpoints 4 epsilon 1 sievetoframe rms :1-279 sieve 10 \
> >>
> >> out dbscan_clust/cnumvtime.dat sil Sil \
> >>
> >> summary dbscan_clust/summary.dat info dbscan_clust/info.dat \
> >>
> >> cpopvtime dbscan_clust/cpopvtime.agr normframe repout
> >> dbscan_clust/rep repfmt pdb \
> >>
> >> singlerepout dbscan_clust/singlerep.nc singlerepfmt netcdf avgout
> >> Avg avgfmt restart
> >>
> >> run
> >>
> >> clear all
> >>
> >>
> >>
> >> The clustering runs OK with no noticeable problems. However, it has me
> >> intrigued to see that unlike all other clustering plots I have seen
> >> (clusters starting at 1), the clusters on this one start from cero. I fail
> >> to find a reason for this behaviour. Find a picture of the pop vs frame I
> >> get at the bottom of this message.
> >>
> >>
> >>
> >> I would really appreciate it if anyone could help me solve this problem
> >>
> >>
> >>
> >> Thank you in advance,
> >>
> >>
> >>
> >> Daniel Fernández
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 Thu Jun 13 2019 - 13:00:04 PDT
