Hi,
What version of cpptraj are you using? Make sure you're using either
the GitHub version (6.19.4) or the AmberTools 23 version (6.18.1) if
you're not already.
-Dan
On Wed, Jun 14, 2023 at 2:06 PM Saikat Pal via AMBER <amber.ambermd.org> wrote:
>
> Dear all,I am trying to perform K-means clustering of my system. I am using the following script:
> trajin remd-3.nc 1 last 10
> strip :Na+,Cl-,WAT
> cluster c1 \
> kmeans clusters 50 randompoint maxit 1000 \
> rms :1-15.C,N,O,CA \
> sieve 10 random \
> 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 pdb
> run
>
> However, I am getting the following errors:ANALYSIS: Performing 1 analyses:
> 0: [cluster c1 kmeans clusters 5 randompoint maxit 1000 rms :1-15.C,N,O,CA sieve 10 random 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 pdb]
> Starting clustering.
> Mask [:1-15.C,N,O,CA] corresponds to 60 atoms.
> RNG: Marsaglia
> Random_Number: seed is <= 0, using wallclock time as seed (1639061)
> Estimated pair-wise matrix memory usage: > 79.664 kB
> Pair-wise matrix set up with sieve, 2000 frames, 200 sieved frames.
> Calculating pair-wise distances.
> 0% Segmentation fault (core dumped)
>
> Please help me to solve the issue.
> Thanks and Regards,
> Saikat Pal
>
>
>
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Received on Wed Jun 14 2023 - 12:00:02 PDT
