CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:06:52 | Available memory: 65.911 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 5 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 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, 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= 52.7051 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 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 (137890000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 11% 20% 31% 41% 50% 61% 71% 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: 495 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 20 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 6 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 2 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% 66% 70% 89% 90% Complete. #Clustering: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.770283 #Cluster 1 has average-distance-to-centroid 0.783189 #Cluster 2 has average-distance-to-centroid 0.868719 #Cluster 3 has average-distance-to-centroid 1.267213 #Cluster 4 has average-distance-to-centroid 1.340347 #DBI: 1.116669 #pSF: 34325.743033 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 8677 47497 2179 76622 5340 #Sieve value: 200 (random) #Sieved frames: 181 525 650 1370 1622 1726 1817 1871 1919 1987 2003 2172 2179 2507 2571 2851 2999 3066 3088 3941 4084 4296 4312 4410 4488 5045 5091 5340 5365 5630 5675 5973 6039 6189 6421 6571 6579 6608 6659 6672 6904 6984 7093 7365 7888 7916 7985 8677 8802 9055 9226 9497 9678 9835 10411 10561 10784 10851 10860 11146 11359 11622 12506 12537 12581 12719 12866 13111 13472 13532 13571 13572 13670 13751 13764 13781 14140 14408 14607 14614 14659 14805 14932 14942 14967 15319 15421 15422 15498 15506 15874 16450 16857 16930 17350 17459 17477 17485 17539 17625 17698 17999 18298 18665 18796 18894 19031 19075 19136 19331 19572 19859 19913 19924 20386 20399 20486 21031 21064 21092 21338 21906 22247 22512 23077 23365 23389 23443 23564 23616 24104 24276 24746 24763 25721 25772 25811 26449 26525 26527 26586 26702 26784 26810 27110 27178 27359 27363 27411 27483 27627 27702 27910 27986 27996 28075 28312 28580 28807 29031 29093 29106 29798 29883 29917 29989 30134 30339 30590 30674 30695 30992 31018 31362 31465 31533 31805 31870 31982 32033 32373 32428 32646 32995 33179 33344 33549 33649 33980 33989 34019 35108 35465 35903 35962 36248 36528 36579 36884 37371 37490 37675 39479 39526 39566 39572 39706 40704 40757 40796 41031 41802 41951 42205 42359 42380 42397 42724 42793 42885 43023 43025 43059 43204 43246 43267 43446 43471 43666 43814 43902 43920 44329 44409 44460 44713 44767 44997 45169 45483 45705 45731 45832 45917 45986 46015 46372 46375 46380 46537 47105 47160 47313 47497 47671 47802 47815 47861 48350 48811 48832 49454 49615 49864 50291 50490 50519 50641 50837 50926 51117 51440 51599 51936 52108 52136 52739 53019 53102 53245 53433 53440 53507 53515 54083 54168 54312 54345 54733 54872 55225 55692 55844 55968 56008 56214 56569 56858 57484 58027 58661 58720 58984 59301 59600 59781 59939 60245 60273 60282 60540 60922 61119 61552 62038 62422 62499 62523 62627 62856 63057 63541 63647 63956 63985 64325 64859 64980 65148 65166 65167 65204 65405 65534 65758 65853 66102 66278 66586 67203 67846 67955 68424 68797 69011 69114 69190 69213 69257 69763 69928 70486 70680 70960 71207 71541 71670 71817 71821 71902 72956 73005 73056 73191 73263 73506 73765 73895 73907 74433 74497 74575 74812 75031 75050 75344 75362 75435 75480 75568 75612 75781 75898 76234 76612 76622 76800 77878 77895 77907 78151 78361 78377 78607 78810 78928 79010 79349 79475 79734 79787 79820 79999 80492 80809 80974 81148 81199 81209 81245 81291 81563 82429 83100 83389 83609 84038 84457 84572 84645 84798 84946 85071 85184 85497 85574 85711 85843 86076 86394 86936 87049 87187 87776 88015 88025 88313 88337 88836 89084 89355 89958 90014 90279 90401 90476 90605 90627 90754 90765 90823 91071 91102 91341 91578 91590 91777 91839 91892 92168 92360 92389 92497 92681 92853 92992 93186 93395 93469 93699 94206 94395 94936 95153 95234 95264 95352 95614 95898 96395 97290 97333 97390 97447 97691 97737 97844 97966 98122 98445 98531 98562 98742 98869 99098 99191 99531 99641 99871 99966 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. : 0.0133 s ( 0.02%) TIME: Pairwise Calc.: 0.4608 s ( 0.81%) TIME: Clustering : 0.0229 s ( 0.04%) TIME: Cluster Post. : 56.6118 s ( 99.13%) TIME: Total: 57.1088 s TIME: Analyses took 57.1291 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 : 1897.3482 s ( 97.06%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 57.1291 s ( 2.92%) TIME: Data File Write : 0.3996 s ( 0.02%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1954.8770 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1981.3221 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.