CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:23:17 | Available memory: 2.140 GB INPUT: Reading input from 'pt-clust.in' [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [trajin ../../../aa/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run1/traj.1.02,../../../aa/tip3p/ff12sb/run1/traj.1.03,../../../aa/tip3p/ff12sb/run1/traj.1.04,../../../aa/tip3p/ff12sb/run1/traj.1.05,../../../aa/tip3p/ff12sb/run1/traj.1.06,../../../aa/tip3p/ff12sb/run1/traj.1.07,../../../aa/tip3p/ff12sb/run1/traj.1.08,../../../aa/tip3p/ff12sb/run1/traj.1.09,../../../aa/tip3p/ff12sb/run1/traj.1.10,../../../aa/tip3p/ff12sb/run1/traj.1.11,../../../aa/tip3p/ff12sb/run1/traj.1.12,../../../aa/tip3p/ff12sb/run1/traj.1.13,../../../aa/tip3p/ff12sb/run1/traj.1.14,../../../aa/tip3p/ff12sb/run1/traj.1.15,../../../aa/tip3p/ff12sb/run1/traj.1.16,../../../aa/tip3p/ff12sb/run1/traj.1.17,../../../aa/tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run2/traj.1.02,../../../aa/tip3p/ff12sb/run2/traj.1.03,../../../aa/tip3p/ff12sb/run2/traj.1.04,../../../aa/tip3p/ff12sb/run2/traj.1.05,../../../aa/tip3p/ff12sb/run2/traj.1.06,../../../aa/tip3p/ff12sb/run2/traj.1.07,../../../aa/tip3p/ff12sb/run2/traj.1.08,../../../aa/tip3p/ff12sb/run2/traj.1.09,../../../aa/tip3p/ff12sb/run2/traj.1.10,../../../aa/tip3p/ff12sb/run2/traj.1.11,../../../aa/tip3p/ff12sb/run2/traj.1.12,../../../aa/tip3p/ff12sb/run2/traj.1.13,../../../aa/tip3p/ff12sb/run2/traj.1.14,../../../aa/tip3p/ff12sb/run2/traj.1.15,../../../aa/tip3p/ff12sb/run2/traj.1.16,../../../aa/tip3p/ff12sb/run2/traj.1.17,../../../aa/tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd :1-2&!@H= first mass] RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit K-MEANS: Looking for 5 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 150000 200000 Cluster trajectories will be written to ctraj, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (rep), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top full.topo.hmr to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [tip3p-ff12sb] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (4 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 2: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 3: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 200000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (3 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Reference mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 2: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (200000 frames): 7.927 GB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% ----- traj.1.01 (1-50000, 1) ----- 30% 40% ----- traj.1.01 (1-50000, 1) ----- 50% 60% 70% ----- traj.1.01 (1-50000, 1) ----- 80% 90% 100% Complete. Read 200000 frames and processed 200000 frames. TIME: Avg. throughput= 602.3733 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (167020000) Estimated pair-wise matrix memory usage: > 1.998 MB Pair-wise matrix set up with sieve, 200000 frames, 1000 sieved frames. 0% 21% 23% 38% 40% 64% 66% 71% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 2.998 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 995 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 74 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 14 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 9 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 13 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 7 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 4 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 24 threads 0% 10% 23% 39% 40% 55% 60% 72% 80% 90% Complete. #Clustering: 5 clusters 200000 frames #Cluster 0 has average-distance-to-centroid 0.851755 #Cluster 1 has average-distance-to-centroid 1.366039 #Cluster 2 has average-distance-to-centroid 1.248825 #Cluster 3 has average-distance-to-centroid 1.525261 #Cluster 4 has average-distance-to-centroid 1.866265 #DBI: 1.443049 #pSF: 58102.092372 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 23843 26432 82263 83127 2772 #Sieve value: 200 (random) #Sieved frames: 13 137 308 440 777 875 946 1124 1198 1261 1276 1397 1555 1558 1788 1910 2068 2114 2165 2210 2563 2648 2655 2772 2960 3113 3175 3353 3379 3507 3830 3914 4090 4461 4736 4834 4975 4995 5012 5035 5125 5180 5241 5806 5822 6066 6305 6362 6538 6923 7251 7873 8108 8182 8358 8479 8503 8612 9005 9235 9622 9763 9799 9983 10166 10177 10203 10250 10305 10531 11568 11674 11837 11903 12025 12039 12245 12541 12630 12935 12944 12975 13024 13157 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Warning: split frame 200000 is out of bounds; ignoring. Writing 'ctraj.c0' as Amber NetCDF Writing 'ctraj.c1' as Amber NetCDF Writing 'ctraj.c2' as Amber NetCDF Writing 'ctraj.c3' as Amber NetCDF Writing 'ctraj.c4' as Amber NetCDF Writing 'rep.c0.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0004 s ( 0.00%) TIME: Pairwise Calc.: 1.8805 s ( 1.45%) TIME: Clustering : 0.1737 s ( 0.13%) TIME: Cluster Post. : 127.6863 s ( 98.42%) TIME: Total: 129.7409 s TIME: Analyses took 129.7439 seconds. DATASETS (4 total): [tip3p-ff12sb] "[tip3p-ff12sb]" (topology), size is 3301 full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent RMSD_00001 "RMSD_00001" (double, rms), size is 200000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 200000 (7.927 GB) Box Coords, 3301 atoms Cnum_00003 "Cnum_00003" (integer), size is 200000 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 332.0200 s ( 71.90%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 129.7439 s ( 28.10%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0160 s ( 0.00%) TIME: Run Total 461.7799 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 462.7880 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.