CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:48:45 | Available memory: 66.007 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] 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 dme :1,2@C5',C4',C3',O3',P,C2 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 DME (mask [:1,2@C5',C4',C3',O3',P,C2]) 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-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] 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= 49.5786 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster dme :1,2@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2] corresponds to 11 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (146760000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 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: 6 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 1 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% 56% 56% 56% 56% 60% 70% 80% 90% Complete. #Clustering: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.353555 #Cluster 1 has average-distance-to-centroid 0.589912 #Cluster 2 has average-distance-to-centroid 0.819256 #Cluster 3 has average-distance-to-centroid 0.623018 #Cluster 4 has average-distance-to-centroid 0.633978 #DBI: 1.360812 #pSF: 44218.696794 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 73687 81849 60133 75736 96530 #Sieve value: 200 (random) #Sieved frames: 105 222 459 510 594 824 1190 1226 1270 1280 1382 1518 1582 1747 2514 2704 2839 2873 3171 3437 3472 3549 3675 3745 3774 4004 4128 4287 4376 4979 5303 5603 5638 5657 5704 5795 6837 7231 7380 7491 7588 7647 8203 8575 9405 9421 9595 9841 9948 10043 10055 10148 10160 10235 10392 10426 10686 10709 10902 10979 11232 11305 11440 12352 12785 13933 13956 14178 14337 14360 14473 14755 14802 14978 14981 15343 15605 15792 15960 16172 16174 16603 16879 17415 17524 18035 18096 18275 18352 18600 18938 18981 19093 19211 19274 19281 19605 19631 20055 20139 20201 20293 20612 20652 20814 20863 20865 20904 21256 21291 21426 21621 21742 21752 21894 22132 22508 22713 22760 22944 23018 23026 23363 23376 23516 23543 23718 23960 24042 24507 24522 24607 24743 24907 25062 25244 25943 25978 26054 26245 26654 26859 26918 26932 27100 27221 27275 27387 27437 27702 27943 28047 28076 28107 28126 28162 28311 28711 28799 29007 29173 29329 29527 29864 29989 30293 30320 30512 30596 30668 31570 32403 32619 32888 32971 33106 33126 33297 33359 33479 33618 33953 33982 34160 34208 34249 34437 34638 34656 35117 35128 35363 35784 36083 36143 36263 36338 36375 36676 36713 36978 37478 37590 37752 38225 38260 38313 38343 38455 38523 38596 38752 39338 39484 39521 39688 39902 40174 40529 40575 40633 40771 40963 40981 41265 41342 41629 41638 42373 42693 42722 42817 43472 43514 43541 43683 43883 43951 44026 44075 44306 44587 45211 45535 45688 46231 46610 47439 47548 47763 47783 48028 48215 48241 48362 48511 48839 48892 48988 49061 49111 49307 49316 49514 49643 50124 50487 50714 50823 51148 51355 51385 51836 52280 52364 52502 52592 52701 53391 53645 53677 53788 53791 53863 54168 54170 54384 54500 54550 54819 55000 55143 55844 55900 56193 56468 56577 56786 56837 57008 57178 57268 57582 57657 57789 58079 58230 58533 58846 58888 58995 59048 59326 59464 59584 59797 60042 60133 60179 60482 60498 60693 60860 61628 61941 62050 62703 62865 62889 63235 63244 63250 63480 64029 64113 64765 65027 65789 66023 66201 66270 66946 66962 67040 67406 67583 67823 67890 68038 68830 69286 69395 69412 69498 69661 69727 69843 69845 69879 70273 70286 70383 70932 71066 71378 71432 71611 71863 71918 71997 72989 73052 73378 73687 74185 74363 74409 74726 75313 75427 75672 75736 75895 76140 76263 76295 76334 76388 76780 76971 77025 77396 77569 77758 78357 78657 79007 79508 80015 80176 80193 80401 80552 80688 81096 81108 81137 81347 81849 81993 82139 82222 82268 82389 82550 82648 82804 82928 83008 83100 83704 84047 84529 84646 84729 85099 85131 85153 85347 86290 86414 86636 86789 87065 87595 87997 88077 88133 88191 88241 88797 88980 89319 89354 89357 89656 89961 90689 90911 91493 91520 91530 91557 91634 91978 92027 92048 92113 92115 92911 93000 93124 93203 93493 93584 93995 94392 94539 94569 94579 94698 94975 95039 95631 95880 95934 96155 96380 96398 96453 96530 96607 96842 97183 97214 97274 97374 97852 98005 98064 98325 98490 98508 98522 98547 98615 98809 99191 99613 99802 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. : 0.0023 s ( 0.00%) TIME: Pairwise Calc.: 0.2272 s ( 0.43%) TIME: Clustering : 0.0160 s ( 0.03%) TIME: Cluster Post. : 52.0538 s ( 99.53%) TIME: Total: 52.2993 s TIME: Analyses took 52.3241 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 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 2016.9978 s ( 97.47%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 52.3241 s ( 2.53%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2069.3221 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2076.0485 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.