CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:08:51 | Available memory: 64.749 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@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2]) 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, 3300 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: 64 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](40) Reference mask: [:1-2&!@H*](40) 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): 79.200 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= 55.5167 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 6 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 (138830000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 21% 30% 41% 51% 61% 71% 81% 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: 494 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 50 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 32 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 22 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 9 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 1 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 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 0.666738 #Cluster 1 has average-distance-to-centroid 0.642170 #Cluster 2 has average-distance-to-centroid 0.745083 #Cluster 3 has average-distance-to-centroid 0.932987 #Cluster 4 has average-distance-to-centroid 1.264808 #Cluster 5 has average-distance-to-centroid 1.158363 #DBI: 1.251798 #pSF: 35028.006830 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 34822 32339 80735 78583 76651 26423 #Sieve value: 200 (random) #Sieved frames: 86 407 408 768 831 879 1073 1446 1644 1873 2667 2765 2916 2979 3033 3141 3254 3338 3416 3492 3565 3610 3620 3793 3978 4188 4560 4567 5002 5098 5227 5254 5360 5366 5628 5701 5711 5836 5893 6120 6145 6460 6597 6655 7115 7273 7731 7781 8623 8727 9017 9322 9855 9869 10336 10515 10658 10977 11710 13164 13876 13933 14333 14338 14383 14656 14738 14912 15274 15301 15891 15934 16273 17034 17212 17532 17985 18117 18358 18434 18484 18665 18902 18946 18977 18998 19046 19233 19790 20207 20706 20833 20878 21233 21265 21317 21560 21643 21965 22284 22469 22607 22690 22832 22972 23688 23949 24432 24720 24822 25262 25281 25530 25583 25632 25701 25788 26025 26402 26423 26437 26669 26957 27138 27169 27329 28250 28256 28319 29009 29165 29903 29973 30479 30543 30710 30769 31192 31233 31260 31347 31420 31431 31497 31831 32339 32359 32526 32626 32802 32967 33421 33423 33593 33870 34539 34822 34871 34954 35059 35078 35178 35210 35232 35426 35428 35663 35678 35741 35823 35853 35994 36165 36278 36434 36551 36568 36865 37143 37321 37322 37541 37645 38177 38381 38452 38524 38873 38888 39813 40186 40404 40500 40520 40633 40684 40689 40819 40835 41130 41486 41651 42187 42506 42618 42936 43002 43175 43218 43289 43427 43438 43625 43978 44197 44362 44530 44858 44885 45270 45826 46188 46428 46669 47497 47498 47596 47604 47784 47858 47971 48070 48390 48408 48478 48524 48592 48739 49020 49041 49062 49140 49262 49362 49507 49512 49553 49987 49989 50293 50750 50773 50921 50960 50964 51235 51508 51518 51815 52017 52380 52577 52734 52823 53183 53251 53596 54016 54209 54524 54785 54960 55040 55257 55295 55431 55663 55718 55758 55768 55894 56390 56421 56469 56514 56611 56802 56828 56869 56977 57308 57588 58083 58131 58346 58416 58423 58507 59281 59860 59942 60253 60290 60443 60535 60882 60906 60946 61097 61111 61503 61589 61702 61970 62267 62428 62797 63137 63166 63714 63728 63807 63854 63953 64149 64188 64345 64597 65389 65411 65591 65714 66197 66571 66815 67357 67660 67776 68241 68622 68727 68865 68868 68983 68987 69193 69229 69820 69863 69958 70149 70217 70487 70575 70928 71231 71447 71573 71588 71857 72003 72221 72354 72432 72568 72614 73147 73231 73380 73466 73546 73913 73962 74394 74436 74437 75075 75211 75356 75731 75976 76631 76650 76651 77144 77190 77385 77665 77711 78163 78427 78583 79046 79130 79367 79411 79859 80002 80006 80206 80567 80610 80703 80735 81008 81315 81439 81473 81744 81906 81991 82152 82200 82257 82583 82612 82627 82788 82986 83485 83569 83784 83799 84309 84608 84641 84688 84916 85155 85268 85604 85854 86022 86342 86508 86751 87356 87519 87700 87701 87841 87863 88139 88239 88582 88670 88762 88998 89030 89065 89159 89251 89462 89723 90731 90888 90890 91172 91346 91645 91655 91867 92060 92247 92281 92304 92549 92890 93130 93417 93436 93455 93535 93610 93823 93880 93911 94162 94243 94469 94925 94975 95192 95218 95343 95652 96379 96885 96915 97249 97310 97469 97610 97778 98132 98494 99124 99179 99367 99567 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. : 0.0133 s ( 0.02%) TIME: Pairwise Calc.: 0.4910 s ( 0.84%) TIME: Clustering : 0.0351 s ( 0.06%) TIME: Cluster Post. : 57.9684 s ( 99.08%) TIME: Total: 58.5078 s TIME: Analyses took 58.5282 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (79.200 MB) Box Coords, 64 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 : 1801.2603 s ( 96.84%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 58.5282 s ( 3.15%) TIME: Data File Write : 0.3004 s ( 0.02%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1860.0890 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1863.1171 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.