CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 12:33:53 | Available memory: 13.424 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 5 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 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-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= 81.2337 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] Starting clustering. Mask [:1,2&!@H*] corresponds to 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (152880000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 10% 21% 31% 40% 50% 61% 71% 80% 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: 495 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 7 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 2 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 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 0.597409 #Cluster 1 has average-distance-to-centroid 1.109651 #Cluster 2 has average-distance-to-centroid 1.411593 #Cluster 3 has average-distance-to-centroid 1.491936 #Cluster 4 has average-distance-to-centroid 1.674369 #DBI: 1.316344 #pSF: 56815.697910 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 47487 8404 47004 82174 48522 #Sieve value: 200 (random) #Sieved frames: 43 186 356 485 730 760 783 969 1024 1029 1227 1370 1854 1902 2162 2269 2383 2611 2678 2699 2747 2761 2971 3171 3365 3475 3915 4284 4405 4543 4651 5089 5237 5394 5475 5991 6173 6404 6848 7009 7023 7649 7834 7843 7906 8157 8177 8233 8404 8574 8955 8974 9079 9232 9241 9423 9446 9466 9674 9720 9738 9818 10249 10257 10266 10421 10426 10531 11251 11369 11404 11615 12040 13001 13238 13517 13519 13566 13724 13775 14089 14241 14394 14427 14429 14465 14481 14689 14969 15163 15167 15983 16010 16385 16410 16413 16553 16692 16699 17074 17080 17399 17424 17546 17941 18207 18715 18819 19228 19375 19404 19444 19500 19605 19770 20357 20596 20812 20907 20935 21041 21089 21183 21369 21429 22067 22168 22838 22867 22957 23037 23134 23497 24235 24295 24300 24307 24433 24663 24908 25055 25147 25542 25684 26023 26206 26442 26486 26787 26810 27060 27149 27162 27739 28081 28542 28604 28708 28751 28964 29049 29658 29955 29984 30758 30819 30965 31108 31252 31254 31956 32131 32259 32376 32705 32759 32964 32968 33011 33990 34361 34889 35147 35386 35471 35510 35838 35883 36141 36457 36674 36906 36941 37022 37153 37572 37585 38323 38525 38674 39232 39325 39415 39586 40142 40171 40209 41405 42265 42429 42432 42494 43209 43315 43438 43451 43549 43730 44458 44520 44648 44702 44758 44779 44827 44921 45134 45277 45367 45401 45923 46248 46371 46562 46576 46741 46834 47004 47487 47707 47736 47989 48123 48125 48219 48245 48297 48522 48530 48554 48704 48909 49063 49280 49512 49784 50554 50740 51085 51111 51357 51699 52159 52190 52458 52574 52884 52965 53201 53300 53872 54103 54164 54290 54467 54922 54938 55071 55261 55359 55724 55755 55921 56408 56592 56704 56751 56923 57035 57132 57296 57402 57553 57996 58272 58343 58393 58519 58608 58613 58688 58950 59077 59917 60093 60259 60784 61014 61933 62043 62376 62390 62424 62664 62681 62723 63021 63099 63663 63685 63785 64261 64441 64461 64881 65072 65309 65389 65435 65495 65632 65765 65920 65966 65972 66022 66167 66177 66340 66391 66573 66733 67057 67078 67181 67263 67276 67327 67385 67807 67870 68393 68619 68822 68835 68888 68906 69026 69067 69068 70105 70249 70661 70771 71328 72109 72132 72464 72484 72631 72722 72824 72959 73136 73148 73753 73881 74431 74704 75186 75342 75343 75489 75532 75806 76147 76218 76232 76251 76283 76545 76662 76774 77286 77366 77395 77454 78109 78135 78581 78616 78726 78793 78927 79045 79411 79419 79567 79573 79631 80006 80358 80368 80399 80840 80935 81291 81681 81902 82174 82194 82439 82883 83019 83224 83375 83503 83794 84268 84286 84378 84845 85017 85104 85298 85369 85455 85457 85492 85746 85756 85796 85824 86281 86319 86582 86713 86723 86785 87896 88769 88872 88908 89098 89137 89236 89335 89365 89384 89423 89484 89595 90294 90433 90477 90738 91148 91273 91561 91628 91763 92065 92245 92316 92594 92606 92841 93573 93973 94162 94466 94534 94738 94763 94785 94953 95268 95492 95661 95754 97194 97416 98094 98190 98345 98404 99204 99517 99762 99858 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. : 0.3168 s ( 0.53%) TIME: Pairwise Calc.: 0.0495 s ( 0.08%) TIME: Clustering : 0.0311 s ( 0.05%) TIME: Cluster Post. : 59.4343 s ( 99.34%) TIME: Total: 59.8316 s TIME: Analyses took 59.8316 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 : 1231.0158 s ( 95.36%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.8316 s ( 4.64%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0105 s ( 0.00%) TIME: Run Total 1290.8579 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1296.2134 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.