CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 12:34:41 | Available memory: 14.189 GB INPUT: Reading input from 'pt-clust.in' [parm ../../tip3p/ff14sb/run1/build/full.topo.hmr [tip3p-ff14sb]] Reading '../../tip3p/ff14sb/run1/build/full.topo.hmr' as Amber Topology [trajin ../../tip3p/ff14sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff14sb/run1/traj.1.02,../../tip3p/ff14sb/run1/traj.1.03,../../tip3p/ff14sb/run1/traj.1.04,../../tip3p/ff14sb/run1/traj.1.05,../../tip3p/ff14sb/run1/traj.1.06,../../tip3p/ff14sb/run1/traj.1.07,../../tip3p/ff14sb/run1/traj.1.08,../../tip3p/ff14sb/run1/traj.1.09,../../tip3p/ff14sb/run1/traj.1.10,../../tip3p/ff14sb/run1/traj.1.11,../../tip3p/ff14sb/run1/traj.1.12,../../tip3p/ff14sb/run1/traj.1.13,../../tip3p/ff14sb/run1/traj.1.14,../../tip3p/ff14sb/run1/traj.1.15,../../tip3p/ff14sb/run1/traj.1.16,../../tip3p/ff14sb/run1/traj.1.17,../../tip3p/ff14sb/run1/traj.1.18 parm [tip3p-ff14sb]] Reading '../../tip3p/ff14sb/run1/traj.1.01' as Amber NetCDF [trajin ../../tip3p/ff14sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff14sb/run2/traj.1.02,../../tip3p/ff14sb/run2/traj.1.03,../../tip3p/ff14sb/run2/traj.1.04,../../tip3p/ff14sb/run2/traj.1.05,../../tip3p/ff14sb/run2/traj.1.06,../../tip3p/ff14sb/run2/traj.1.07,../../tip3p/ff14sb/run2/traj.1.08,../../tip3p/ff14sb/run2/traj.1.09,../../tip3p/ff14sb/run2/traj.1.10,../../tip3p/ff14sb/run2/traj.1.11,../../tip3p/ff14sb/run2/traj.1.12,../../tip3p/ff14sb/run2/traj.1.13,../../tip3p/ff14sb/run2/traj.1.14,../../tip3p/ff14sb/run2/traj.1.15,../../tip3p/ff14sb/run2/traj.1.16,../../tip3p/ff14sb/run2/traj.1.17,../../tip3p/ff14sb/run2/traj.1.18 parm [tip3p-ff14sb]] Reading '../../tip3p/ff14sb/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&!@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-ff14sb] full.topo.hmr, 3319 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 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 3256 atoms. Stripped topology: 63 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): 78.000 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= 81.4687 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 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (153000000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 21% 30% 41% 51% 60% 71% 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: 494 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 8 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 5 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 1 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 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 0.576675 #Cluster 1 has average-distance-to-centroid 1.016675 #Cluster 2 has average-distance-to-centroid 1.134524 #Cluster 3 has average-distance-to-centroid 1.346624 #Cluster 4 has average-distance-to-centroid 1.433833 #Cluster 5 has average-distance-to-centroid 1.718851 #DBI: 1.501323 #pSF: 47274.041180 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 83228 95140 44461 2866 83343 5017 #Sieve value: 200 (random) #Sieved frames: 107 122 716 720 1161 1194 1466 1621 1819 2362 2536 2663 2783 2866 3131 3166 3216 3434 3487 3661 4086 4764 5017 5284 5290 5874 6235 6639 6646 7114 7245 7389 7593 7719 7776 8057 8645 8946 8987 9548 9757 9931 10193 10275 10538 10686 10697 10970 11060 11249 11302 11327 11966 12334 12683 12808 13486 13695 13773 13787 13944 13967 14158 14312 14379 14470 14649 14811 15209 15401 15525 15721 15772 15818 16101 16111 16281 17111 17141 17430 17540 17803 17896 18294 18583 19961 20232 20346 20358 21109 21186 21474 21622 21778 22079 22262 22371 23545 24091 24623 25060 25125 25257 25336 25374 25393 25436 25572 25933 25957 26022 26266 26375 26483 26719 26946 27035 27186 27285 27351 27724 27801 27941 27949 28022 28324 28695 28838 28866 29429 29432 29614 29956 30559 30736 30857 31146 31344 31468 31568 31805 32114 32855 32885 33142 33449 33501 33539 33665 33804 34243 34845 35212 35812 35823 35974 36406 36526 36703 37256 37262 37377 37476 37577 37687 37907 38007 38033 38120 38471 38855 39062 39172 39235 39701 39712 39741 39790 39793 39863 39890 39927 39940 39971 39992 40058 40493 40668 40754 40802 40939 40988 42204 42241 42326 42430 42991 43228 43252 43326 43516 43826 44046 44201 44318 44461 44472 44999 45099 45126 45192 45296 45778 45910 45946 46182 46697 46778 46838 47131 47421 47700 47710 47720 47941 47942 48188 48232 48597 48711 48756 48794 48849 49051 49297 49442 49646 49735 49762 49925 50209 50392 50496 50711 50783 51045 51120 51285 51460 51497 51637 51676 51710 51868 51964 52025 52045 52331 53231 53622 53640 53798 54506 54644 54959 54990 55064 55264 55323 55741 55856 55937 56033 56246 56277 56313 56331 56600 56676 57432 57498 57601 57840 57978 58522 58793 58919 59010 59248 59603 59684 59781 59798 59800 59802 60014 60051 60376 60417 60599 61574 61665 62053 62126 62145 62971 63713 64411 64546 64810 65251 65296 65393 65423 65741 65794 65806 65986 66098 66208 66321 66646 66897 66960 67449 67644 67985 68102 68165 68586 68713 68727 69363 69453 69682 69794 69855 70141 70188 70356 70466 70516 70521 70568 70615 70968 71208 72037 72447 72743 73103 73126 73255 73401 73416 73505 73883 73967 74745 74863 74970 75005 75184 75284 75307 75334 75432 75570 75585 75818 76066 76426 76476 76563 76931 77207 77310 77372 77907 78239 78272 78356 78688 78807 79010 79140 79271 79309 79346 79517 79741 80441 81029 81366 81448 82034 83074 83154 83228 83343 83446 83690 83756 83772 83946 84280 84313 84340 84470 84533 84820 85003 85079 85491 85835 85852 86134 86203 86388 86396 86650 86711 86833 86893 86959 87023 87214 87326 87386 87534 87547 87655 87818 88486 88497 88583 88815 88895 88932 89243 89419 89520 89767 90245 90406 90407 90682 90706 90868 90980 91005 91007 91025 91049 91218 91316 91323 91431 91732 91788 91902 91940 92109 92114 92195 92200 92218 92602 92693 92769 92933 93234 93235 93270 93309 93401 93455 93520 93633 93933 95140 95180 95268 95407 95648 96424 96855 97074 97247 97306 97553 97665 97778 98169 98219 98285 98337 98590 99183 99375 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. : 0.3214 s ( 0.54%) TIME: Pairwise Calc.: 0.0533 s ( 0.09%) TIME: Clustering : 0.0443 s ( 0.07%) TIME: Cluster Post. : 58.7231 s ( 99.29%) TIME: Total: 59.1421 s TIME: Analyses took 59.1422 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (78.000 MB) Box Coords, 63 atoms Cnum_00003 "Cnum_00003" (integer), size is 100000 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1227.4658 s ( 95.40%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.1422 s ( 4.60%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1286.6081 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1287.4457 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.