CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:19:31 | Available memory: 7.253 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 7 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 7 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= 551.9801 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 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Loading pair-wise distances from CpptrajPairDist Loading pair-wise distances failed - regenerating from frames. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (188190000) Estimated pair-wise matrix memory usage: > 1.998 MB Pair-wise matrix set up with sieve, 200000 frames, 1000 sieved frames. 0% 10% 21% 32% 41% 52% 62% 71% 80% 92% 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: 993 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 77 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 24 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 33 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 32 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 15 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 2 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% 11% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 7 clusters 200000 frames #Cluster 0 has average-distance-to-centroid 0.810076 #Cluster 1 has average-distance-to-centroid 1.282242 #Cluster 2 has average-distance-to-centroid 0.794021 #Cluster 3 has average-distance-to-centroid 1.089598 #Cluster 4 has average-distance-to-centroid 1.400583 #Cluster 5 has average-distance-to-centroid 1.576154 #Cluster 6 has average-distance-to-centroid 1.575900 #DBI: 1.350662 #pSF: 56519.655218 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 189126 63369 182011 143647 130693 32326 18831 #Sieve value: 200 (random) #Sieved frames: 176 420 693 823 896 950 1013 1046 1253 1377 1495 1725 1807 1924 2175 2227 2323 2343 3388 3558 3595 3832 4507 4687 4831 5070 5077 5156 5822 5937 6004 6024 6192 6317 6380 6401 6481 6568 6844 7086 7095 7175 7353 7600 7759 8033 8164 8284 8377 8496 8669 8836 8894 8993 9174 9885 10022 10063 10071 10368 10480 10886 11097 11238 11535 11827 12289 12578 12852 13059 13350 13512 13754 13800 14040 14320 14335 14427 14603 14674 14746 14847 14883 15039 15296 15452 15614 15629 15653 15792 16509 16597 16832 17496 17617 17978 18004 18760 18831 18895 19037 19124 19300 19640 19662 20751 20876 20949 21379 21640 21648 22409 22521 22533 22803 22936 23136 23141 23176 23282 23309 23679 23763 23780 23993 24071 24189 24227 24487 24620 24788 24822 24958 26449 26895 26921 27054 27160 27293 27350 27441 27752 27812 28048 28112 28129 28184 28355 29432 29579 29644 30200 30392 30396 30470 30731 30885 31382 31392 31750 31766 31768 31876 31973 32093 32326 32347 32352 32518 32938 32965 33098 33818 34396 34518 34701 34793 34903 34951 35333 35437 35629 35785 35906 36334 36355 36428 36495 36596 36743 36816 36921 37033 37489 37765 37847 38398 38480 38533 39145 39515 39754 39777 40009 40157 40191 40376 40420 40580 40624 40766 40803 40823 41239 41284 41763 41863 41916 41944 42104 42114 42556 42721 42940 43057 43849 43955 44325 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166345 167076 167517 167657 167662 167832 167939 168755 169060 169179 169531 170026 170037 170182 170515 170619 170780 170996 170998 171354 171443 171938 172117 172487 172716 172770 173029 173331 173413 173449 173501 173619 173804 174060 174098 174381 174559 174602 175358 175532 175697 176136 176764 176806 176833 177181 177465 177521 177647 178051 178392 178603 178730 178856 178886 178937 178977 179094 179311 179511 179587 179715 179929 180001 180495 180538 180543 180587 180721 180804 180858 181471 181781 181853 181995 182011 182276 182349 182490 182497 183038 183700 183821 184093 184224 184433 184582 184713 184716 184717 184819 184837 184923 185373 185448 185597 185961 185971 186071 186409 186513 186796 187415 187437 187867 188067 188242 188393 188412 188596 188608 188866 189126 189388 189474 189476 189643 189824 189877 189951 190166 190519 190720 191153 191887 192015 192361 192388 192526 192670 192920 193027 193118 193682 193977 194365 194378 194722 194816 194992 195216 195271 195432 195558 195717 195781 195929 196007 196372 196990 197214 197409 197500 197857 198385 198443 198710 199079 199451 199734 199845 199957 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 'ctraj.c5' as Amber NetCDF Writing 'ctraj.c6' 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. Writing 'rep.c5.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c6.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0130 s ( 0.01%) TIME: Pairwise Calc.: 2.8224 s ( 1.85%) TIME: Clustering : 0.1530 s ( 0.10%) TIME: Cluster Post. : 149.9049 s ( 98.05%) TIME: Total: 152.8933 s TIME: Analyses took 152.8937 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 : 362.3319 s ( 70.32%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 152.8937 s ( 29.67%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0333 s ( 0.00%) TIME: Run Total 515.2590 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 519.0897 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.