CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:36:46 | Available memory: 15.949 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 4 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 4 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= 81.5044 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 4 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 (154030000) 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% 40% 50% 62% 70% 80% 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: 496 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: 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: 4 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.617050 #Cluster 1 has average-distance-to-centroid 1.166737 #Cluster 2 has average-distance-to-centroid 1.847618 #Cluster 3 has average-distance-to-centroid 1.403127 #DBI: 1.209485 #pSF: 66928.632482 #Algorithm: Kmeans nclusters 4 maxit 100 #Representative frames: 345 3838 19431 19054 #Sieve value: 200 (random) #Sieved frames: 345 459 614 722 1345 1647 1839 2179 2290 2298 2463 2725 2774 2879 3060 3482 3591 3686 3838 3885 3968 4055 4057 4538 4691 4783 5500 5669 6083 6829 7112 7218 7659 7684 7833 8121 8228 8663 8690 8823 8901 10047 10331 10447 10558 10791 10905 11061 11192 11236 11765 12051 12456 12523 13000 13028 13098 13230 13874 13893 13901 13933 13985 14070 14561 14601 14797 15185 15527 15597 15802 15843 16122 16591 16658 16710 16731 17070 17350 17515 17639 17834 18568 18738 18763 18866 19054 19297 19431 20018 20191 20268 20306 20415 20553 20888 20996 21241 21352 21418 21594 21803 22123 22161 22261 22761 23103 23527 23947 24165 24244 24332 24459 24639 24677 24898 24965 25108 25449 25581 25620 25674 25838 26124 26491 26916 27036 27076 27192 27232 27533 27554 28358 28666 28917 29098 29681 29697 29728 30072 30198 30314 30351 30387 30767 31101 31541 31554 31678 31988 32362 32640 32678 32687 32763 32827 32934 33218 33270 33349 33525 33736 33897 34236 34271 34524 35007 35136 35322 35495 35836 36302 36799 36974 36982 37256 37676 37684 37822 38020 38033 38401 38587 38637 38704 38837 39126 39255 39432 39650 39909 39924 39947 40128 40364 40440 40580 40606 40881 40948 41363 41491 41780 41834 42130 42610 42614 42638 42647 42663 42748 42768 42912 43371 43557 43646 44087 44360 44630 44729 44929 45129 45146 45253 45683 45950 46407 46535 46570 46771 47024 47039 47218 47286 47678 47929 48393 48408 48436 48916 48966 49140 49141 49240 49488 49766 49787 49844 50502 50583 50801 51018 51162 51205 51723 51752 51825 52036 52141 52409 52524 52572 52730 52759 52801 53019 53496 53813 54363 54643 54829 54881 54891 55392 56267 56591 56644 56781 56814 56877 56932 57669 57882 57912 58405 58499 58570 58572 58812 59080 59146 59293 59356 59501 59583 59780 59804 59847 59987 60026 60049 60618 60786 60994 61003 61147 61161 61163 61181 61384 61686 61760 61987 62295 62754 62962 63318 63404 63488 63786 64292 64296 64412 64763 64977 65160 65261 65588 65691 65827 65956 66281 66476 66561 66658 66671 66767 67018 67069 67111 67185 67290 67458 67488 67760 68134 68259 69042 69091 69652 69827 69977 70170 70177 70338 70621 70751 70940 71019 71123 71354 71585 72787 73520 73728 74047 74063 74114 74118 74437 75140 75202 75285 75573 75814 75866 76046 76185 76211 76317 76419 76499 76969 77040 77652 77721 77887 77927 77937 78171 78177 78225 78292 78912 79050 79334 79627 79705 79806 80193 80275 80301 80502 80553 80562 80601 81346 81631 81667 81767 81787 82182 82722 83139 83309 83337 83425 83725 83742 83756 83772 83938 84176 84406 84449 84504 85298 85644 85706 85914 87206 87252 87502 87865 88239 88306 88374 88541 89109 89112 89639 89904 90054 90361 90363 91083 91108 91159 91173 91295 91351 91459 91460 91589 92098 92169 92204 92779 93111 93265 93517 93636 93881 94009 94050 94514 94923 94958 95253 95286 95469 95564 95733 95877 95905 95985 96211 96376 96403 96670 96693 96798 96818 96856 96914 96975 97020 97402 97634 97788 98036 98218 98757 98788 98849 99098 99179 99500 99631 99990 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 '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. Cluster timing data: TIME: Cluster Init. : 0.3186 s ( 0.53%) TIME: Pairwise Calc.: 0.0507 s ( 0.08%) TIME: Clustering : 0.0208 s ( 0.03%) TIME: Cluster Post. : 60.1583 s ( 99.36%) TIME: Total: 60.5485 s TIME: Analyses took 60.5485 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 : 1226.9283 s ( 95.30%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 60.5485 s ( 4.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1287.4769 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1288.5279 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.