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 - 11:30:02 PDT
