[mahendra@localhost test_folder_openMP]$ cpptraj.OMP -i input_for_test_cpptraj_openMP -p test.top CPPTRAJ: Trajectory Analysis. V14.22 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ Reading 'test.top' as Amber Topology INPUT: Reading Input from file input_for_clustering_by_cpptraj [trajin test_250000frames.pdb 1 10000] Reading 'test_250000frames.pdb' as PDB [loadtraj name MYTRAJ] Saving currently loaded input trajectories as data set with name 'MYTRAJ' [cluster crdset MYTRAJ :1-500@CA,N,C,O mass clusters 10 out cluster_out nofit averagelinkage summary summary_out sieve 30 info Cluster_info repout box2.rep repfmt pdb clusterout cluster.nc clusterfmt netcdf] Warning: No clustering algorithm specified; defaulting to 'hieragglo' CLUSTER: Using coords dataset MYTRAJ, clustering using RMSD (mask [:1-500@CA,N,C,O]), mass-weighted, no fitting Hierarchical Agglomerative: 10 clusters, average-linkage. Initial clustering sieve value is 30 frames. Cluster # vs time will be written to cluster_out Cluster information will be written to Cluster_info Summary of cluster results will be written to summary_out Cluster trajectories will be written to cluster.nc, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (box2.rep), format PDB [go] ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 1 analyses: 0: [cluster crdset MYTRAJ :1-500@CA,N,C,O mass clusters 10 out cluster_out nofit averagelinkage summary summary_out sieve 30 info Cluster_info repout box2.rep repfmt pdb clusterout cluster.nc clusterfmt netcdf] Starting clustering. Mask [:1-500@CA,N,C,O] corresponds to 2044 atoms. Calculating pair-wise distances. Pair-wise matrix set up with sieve, 10000 frames, 334 sieved frames. 0% Floating point exception (core dumped)