CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:37:43 | Available memory: 16.018 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 ../../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. [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [rmsd :1-2&!@H= first mass out test.dat] 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 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit K-MEANS: Looking for 6 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 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, 3300 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (2 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 Coordinate processing will occur on 100000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 64 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](40) Reference mask: [:1-2&!@H*](40) 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. 3: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (100000 frames): 79.200 MB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% ----- traj.1.01 (1-50000, 1) ----- 50% 60% 70% 80% 90% 100% Complete. Read 100000 frames and processed 100000 frames. TIME: Avg. throughput= 25.6935 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 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] Starting clustering. Mask [:1,2&!@H*] corresponds to 40 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (147940000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 21% 31% 41% 50% 62% 71% 81% 90% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 999.160 kB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 494 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 30 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 28 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 49 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 50 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 3 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 3 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 2 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 6 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.656741 #Cluster 1 has average-distance-to-centroid 0.905123 #Cluster 2 has average-distance-to-centroid 0.983512 #Cluster 3 has average-distance-to-centroid 1.658536 #Cluster 4 has average-distance-to-centroid 1.598115 #Cluster 5 has average-distance-to-centroid 1.485788 #DBI: 1.246121 #pSF: 42614.344226 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 35672 86509 11871 32530 12110 69896 #Sieve value: 200 (random) #Sieved frames: 87 140 333 430 562 797 947 961 1091 1096 1130 1208 1603 1616 1947 2277 2391 2406 2455 2908 2965 3321 3520 4186 4227 4440 4514 4769 4946 4972 5119 5184 6408 6603 6643 6732 6847 6919 6953 7007 7486 7549 7756 8413 8595 8606 8632 8825 8949 9355 9508 9571 9830 9833 10172 10278 10312 10720 10781 10798 10880 10993 11055 11134 11533 11820 11871 11945 12110 12719 12860 12956 13063 13184 13381 14133 14210 14406 14432 15009 15704 16229 16280 16762 16772 17750 18158 18454 18763 18787 19338 19453 19809 19878 20143 20237 20523 20684 21596 21638 21930 22076 23547 23590 23892 23981 24105 24150 24264 24266 24331 24508 24776 24790 24808 24948 25221 25265 25346 25487 25778 25779 25820 25991 26100 26272 26313 26459 26461 26497 26522 26823 26883 26968 27206 27526 28542 28761 29090 29115 29214 29343 29945 30301 30901 30937 30948 31276 31330 31545 32013 32296 32309 32350 32377 32530 32538 32550 32770 32923 33062 33128 33227 33700 33946 34063 34107 34111 34439 34542 34574 35268 35672 35922 36171 36432 36664 36825 37116 37748 37883 37942 37949 38145 38234 38331 38472 38503 38620 38639 38821 38999 39039 39112 39299 39741 39750 39811 40119 40130 40290 40412 40875 40906 41306 41470 41891 42177 42461 42508 42701 42777 42850 42877 42923 43177 43651 43693 43795 44151 44358 44724 44785 44834 45051 45451 45475 45556 45648 45732 45818 45820 45902 46286 46574 46805 46913 47027 47138 47201 47228 47359 47479 47824 47841 47917 48203 48460 48520 48533 48535 49253 49305 49638 49676 49865 50001 50922 51204 51286 51617 51841 52385 52783 52932 53109 53131 53426 53722 53754 53873 54023 54072 55245 55311 55375 55413 55814 56019 56196 56369 56477 56593 56617 56655 56832 56922 56991 57134 57184 57460 57931 58411 58953 59506 59654 60060 60221 60272 60490 60501 60574 60760 61260 61507 61693 61803 61953 62011 62097 62172 62499 62680 62857 63062 63169 63201 63215 63345 63653 63706 63800 64040 64056 64401 64402 64805 64984 65760 65853 66225 66654 67353 67749 67893 67897 68197 68243 68520 68549 68960 69027 69896 70300 70467 70499 70685 70788 71086 71172 71627 71837 71930 72004 72064 72486 72513 72750 72913 73036 73238 73359 73996 74294 74546 74700 74830 74935 75407 75470 75531 75824 75932 75957 76143 76150 76397 76650 77321 77368 77453 77487 77619 77642 78124 78218 78416 78452 79144 79154 79504 79685 79808 79850 79867 80121 80127 81155 81415 81525 81558 81586 82500 82552 82588 82625 82756 82988 83125 83695 83721 83929 83957 83959 84253 84584 84633 84946 85288 85289 86109 86233 86245 86397 86491 86509 86668 86698 86798 86959 87108 87177 87387 87418 87913 87978 88227 88233 88288 88372 88626 88640 88741 89258 89380 89515 89630 89753 90058 90140 90356 90403 90505 90671 90920 91226 91563 91651 91823 91978 92527 92916 93460 93468 93702 94101 94134 94253 94271 94392 94525 94983 95103 95451 95470 95509 95597 95859 95906 96199 96306 96632 96831 96924 96986 97255 97706 97836 98397 98462 98500 98659 98706 98735 98932 99123 99273 99581 99719 99821 Warning: split frame 100000 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 '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. Cluster timing data: TIME: Cluster Init. : 0.3269 s ( 0.55%) TIME: Pairwise Calc.: 0.0817 s ( 0.14%) TIME: Clustering : 0.0773 s ( 0.13%) TIME: Cluster Post. : 58.9945 s ( 99.18%) TIME: Total: 59.4804 s TIME: Analyses took 59.4804 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (79.200 MB) Box Coords, 64 atoms Cnum_00003 "Cnum_00003" (integer), size is 100000 DATAFILES (1 total): test.dat (Standard Data File): RMSD_00001 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 3892.0400 s ( 98.49%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.4804 s ( 1.51%) TIME: Data File Write : 0.1381 s ( 0.00%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 3951.6591 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3961.9917 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.