CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:35:12 | Available memory: 16.014 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, 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 out test.dat] 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= 26.5162 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 (148840000) 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% 40% 50% 62% 70% 82% 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: 12 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 10 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 3 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 0.584103 #Cluster 1 has average-distance-to-centroid 0.980775 #Cluster 2 has average-distance-to-centroid 1.233641 #Cluster 3 has average-distance-to-centroid 1.413859 #Cluster 4 has average-distance-to-centroid 1.167136 #Cluster 5 has average-distance-to-centroid 1.495131 #DBI: 1.188310 #pSF: 48893.158777 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 30018 66347 13788 89405 87269 83788 #Sieve value: 200 (random) #Sieved frames: 384 411 636 985 1204 1219 1294 1712 1927 1967 2056 2061 2563 2700 2705 2878 2988 3261 3451 3586 4335 4524 4916 5045 5287 5313 5314 5393 5492 5539 5639 5668 5862 6080 6134 6892 7022 7139 7261 7268 7479 7572 7605 7614 7705 7934 7999 8043 8079 8163 8895 9309 9784 9797 9934 10020 10037 10169 10228 11740 12199 12314 12351 12753 13005 13222 13307 13788 14002 14253 14913 14925 14939 14995 15413 15475 15548 15556 16394 16622 16669 16713 16922 17009 17248 17589 17961 18149 18357 18401 18443 18747 18864 19652 19952 19982 20082 20386 20397 20434 20535 21426 21701 21706 21939 21948 22009 22044 22312 22657 22677 23013 23194 23566 23609 23801 24217 24310 24459 24797 25807 25861 25945 26043 26381 26464 26528 26883 27116 27117 27694 28130 28430 28528 29115 29251 29376 29817 29842 30018 30184 30338 30451 30670 30704 30710 30947 30990 31558 31712 31723 31884 31886 31946 32169 32173 32375 32417 32679 32774 32790 32825 32905 33206 33209 33288 33553 33778 34119 34120 34835 34968 34981 35104 35275 35408 35989 36050 36306 36854 36935 36938 37046 37603 37633 38060 38213 38594 39484 39784 39787 40112 40767 40886 40981 41517 41876 41926 41969 42188 42638 42727 42925 42933 43052 43126 43385 43955 44017 44119 44217 44314 44724 44754 44914 45211 45572 45605 45929 46276 46495 46528 46568 46849 47455 47518 47553 47636 47999 48067 48278 48292 48560 48858 49058 49126 49395 49734 49804 49807 50069 50110 50172 50662 50747 50788 50865 51132 51295 52021 52106 52180 52190 52436 53083 53150 53325 53359 54271 54525 54600 54679 54836 55041 55221 55234 55371 55901 56014 56782 56794 56870 57203 57701 57746 57869 58034 58195 58233 58473 58525 58957 59490 59624 59651 59736 59823 60500 60536 60561 60587 60655 60710 60752 60785 60947 61715 62235 62396 62455 62874 63168 63222 63272 63373 63426 63520 63634 63642 63943 64176 64207 64340 64379 64450 64902 64940 65067 65250 65360 65640 65748 65945 66057 66133 66347 66440 66852 66989 67267 67415 68354 68593 68773 68957 69183 69223 69405 69410 70198 70210 70294 70608 70643 70848 70905 70916 71598 71614 71765 72109 72166 72191 72233 72246 72359 72668 72882 73003 73072 73191 73203 73427 73707 74310 74425 74462 74615 74791 74851 74984 75355 75592 75637 75783 75933 76146 76453 76665 76744 77356 77444 77574 78283 78318 78456 78909 78941 79000 79135 79245 79358 79990 80170 80174 80202 80220 80227 80538 80670 80906 80916 80966 81103 82062 82597 82966 82998 83119 83391 83453 83788 83926 84448 84714 84767 84882 84886 85054 85536 85806 86102 86275 86460 86758 86915 87005 87269 87436 87457 87605 87773 87983 88507 88584 88737 88890 88935 89098 89103 89150 89197 89299 89405 89419 89441 89882 90012 90029 90045 90083 91146 91298 91384 91689 92032 92696 93452 93793 94154 94266 94527 94692 94708 94784 94919 94963 94983 95084 95298 95304 95374 95418 95657 95720 96026 96083 96204 96232 96426 97158 97414 97423 97742 97754 97760 97959 98319 98374 98696 98700 98734 98740 98741 98994 99128 99563 99688 99713 99904 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. : 0.3811 s ( 0.65%) TIME: Pairwise Calc.: 0.0666 s ( 0.11%) TIME: Clustering : 0.0426 s ( 0.07%) TIME: Cluster Post. : 58.2540 s ( 99.17%) TIME: Total: 58.7442 s TIME: Analyses took 58.7443 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 DATAFILES (1 total): test.dat (Standard Data File): RMSD_00001 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 3771.2761 s ( 98.46%) TIME: Action Post : 0.0052 s ( 0.00%) TIME: Analysis : 58.7443 s ( 1.53%) TIME: Data File Write : 0.1409 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 3830.1666 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3838.1308 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.