CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:51:10 | Available memory: 15.281 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] 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@C5',C4',C3',O3',P,C2 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] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2@C5',C4',C3',O3',P,C2]) 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 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, 3296 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: 60 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](37) Reference mask: [:1-2&!@H*](37) 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): 74.400 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= 86.3407 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2@C5',C4',C3',O3',P,C2 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] Starting clustering. Mask [:1,2@C5',C4',C3',O3',P,C2] corresponds to 11 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (150790000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 21% 31% 42% 51% 61% 72% 81% 91% 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: 495 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 27 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 1 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 7 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 4 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 2 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 1 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 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.414058 #Cluster 1 has average-distance-to-centroid 0.599811 #Cluster 2 has average-distance-to-centroid 0.938137 #Cluster 3 has average-distance-to-centroid 1.111815 #Cluster 4 has average-distance-to-centroid 1.159788 #DBI: 1.208115 #pSF: 50651.538341 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 55744 2702 98185 56555 66116 #Sieve value: 200 (random) #Sieved frames: 51 415 520 595 768 800 1470 1491 1585 1650 1699 1842 2033 2118 2524 2613 2702 2890 3049 3051 3290 3662 3836 4322 4399 4485 4968 4971 5046 5091 5200 5209 5432 5543 5694 5707 5810 5830 5920 5928 6074 6183 6446 6510 6553 6578 6633 6646 6804 7311 7423 7943 8402 8439 8462 8467 8521 8790 8811 9149 9286 9316 9606 9672 9704 9715 9862 9970 10153 10282 10361 10389 10446 10694 11016 11067 11117 11123 11212 11397 11569 11725 11983 12298 12514 12708 13521 14014 14034 14084 14387 14633 14831 14978 15329 15600 15763 16006 16027 16474 16612 16758 16899 16933 17424 17514 17667 17943 18576 18836 18899 19068 19860 20013 20238 20279 20419 21126 21203 21619 21681 22288 22410 22503 22817 23169 23345 23353 23388 23658 23854 24070 24155 24307 24848 25017 25060 25599 25619 25667 25853 26018 26308 26470 26638 26721 27025 27126 27295 27319 27664 27786 28167 28976 29167 30012 30267 30282 30351 30496 30546 30817 31750 31916 32229 32585 32623 32656 32953 32984 33061 33259 33352 33439 33917 33926 33945 34478 34537 34699 34783 34794 35313 35342 35504 35530 35637 35915 36436 36442 36538 36966 37075 37733 37922 38012 38058 38137 38358 38760 38909 39483 40041 40089 40987 41099 41925 42318 42395 42423 42928 43040 43043 43163 43644 43666 43886 44067 44173 44417 44534 44601 44775 45004 45050 45185 45235 45648 45704 45740 45958 46115 46251 46571 46614 46841 47729 47969 48337 48472 48525 48839 48868 49122 49357 49358 49829 50123 50196 50404 50542 52303 52373 52406 52440 52475 52693 53072 53238 53496 53643 53807 54252 54263 54498 55417 55656 55698 55744 56017 56533 56555 56700 56711 56740 56752 56905 57588 57613 58249 58505 58705 59034 59500 59535 59852 60027 60430 60571 60612 60736 60884 61020 61355 61410 61913 62029 62051 62056 62115 62265 62271 62289 62374 63010 63294 63402 63818 63847 63900 63978 64650 64685 64970 65046 65288 65888 65919 65922 66116 66278 66683 67028 67283 67303 67328 67388 67463 67586 67729 67912 68194 68220 68261 68278 68319 68474 68634 68721 68931 69026 69566 69654 69709 69857 70008 70089 70425 70519 70668 70677 70900 71075 71115 71169 71288 71432 71455 71651 71745 71930 72004 72124 72815 72819 73149 73430 73539 74002 74006 74332 74392 74669 75030 75090 75113 75402 76307 76329 76401 76435 76735 76819 76898 77298 77624 77806 77915 78181 78384 78404 78516 78643 78663 78694 78710 78802 78856 78869 78875 79124 79142 79225 79375 79519 80183 80285 80729 80936 81300 81497 82048 82207 82243 82268 82445 82771 82949 83222 83254 83593 83808 84092 84108 84213 84591 85045 85211 85227 85241 85267 85292 85648 86190 86647 87263 87381 87581 87910 88023 88112 88256 88449 88452 88476 88924 89141 89210 89291 89371 89534 89604 89611 89981 90077 90403 90419 90560 91131 91173 91237 91299 91392 91594 91986 92070 92160 92249 92295 92313 92436 92666 92918 93156 93670 93784 93926 93929 94004 94024 94232 94432 94949 95141 95805 96221 97054 97541 97603 98170 98185 98232 98454 98670 98953 99168 99438 99506 99676 99972 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 '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. : 0.3488 s ( 0.59%) TIME: Pairwise Calc.: 0.0442 s ( 0.08%) TIME: Clustering : 0.0417 s ( 0.07%) TIME: Cluster Post. : 58.3585 s ( 99.26%) TIME: Total: 58.7932 s TIME: Analyses took 58.7932 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (74.400 MB) Box Coords, 60 atoms Cnum_00003 "Cnum_00003" (integer), size is 100000 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1158.2028 s ( 95.17%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 58.7932 s ( 4.83%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1216.9962 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1221.6627 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.