CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:42:54 | Available memory: 66.304 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&!@H= 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&!@H=]) 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= 45.7015 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster dme :1,2&!@H= 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&!@H*] corresponds to 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (138910000) 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: 23 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 8 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 16 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: 11 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 14 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 8 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 2 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 1 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 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: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.574498 #Cluster 1 has average-distance-to-centroid 0.689875 #Cluster 2 has average-distance-to-centroid 1.077764 #Cluster 3 has average-distance-to-centroid 1.007056 #Cluster 4 has average-distance-to-centroid 1.010712 #DBI: 1.540127 #pSF: 55809.990586 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 81949 2744 87927 28469 75931 #Sieve value: 200 (random) #Sieved frames: 256 376 798 1221 1434 1619 1627 1893 1975 2338 2452 2744 2772 3298 3344 4104 4232 5340 5624 6166 6209 6299 6828 7100 7214 7234 7543 7563 7749 7790 8023 8142 8160 8362 9678 9877 10106 10690 10731 10864 10997 11062 11108 11207 11291 11416 11747 12571 12923 13010 13253 13281 13313 13343 13442 13700 14181 14522 14547 15105 15159 15224 15253 15306 15399 15664 15748 15766 16449 16861 16877 16895 17263 17479 17659 18178 18251 18404 18494 18763 18789 18868 18885 18898 19093 19191 19207 19557 19715 19800 19966 19994 20116 20433 20454 20927 21248 21420 22691 23046 23109 23375 23505 23508 23715 23799 24163 24317 24470 24674 24803 24828 25045 25071 25449 25498 25572 25815 26045 26391 26470 26990 27127 27455 27582 28364 28469 28788 28853 29080 29137 29341 29363 29653 29712 29926 30029 30644 30711 30846 30981 31261 31271 31628 31639 31664 32079 32354 32377 32416 32499 32558 32565 32660 33237 33343 33462 33493 33559 33676 33882 34243 34457 34660 34735 34823 34904 35063 35501 35898 36229 36308 36371 36514 36697 36970 37588 37783 38024 38259 38856 38896 39187 39200 39209 39406 39732 39787 39969 40217 40778 41004 41088 41321 41366 41861 41903 42176 42383 42398 42612 43147 43426 43534 44359 44462 44504 44573 44779 45014 45134 45619 46118 46374 46624 46660 46672 46688 46838 47177 47237 47585 47983 48035 48137 48551 48816 48976 49156 49631 49650 49712 49808 50089 50382 50460 50568 50645 51024 51599 51641 51643 52049 52108 52195 52201 52300 52594 52621 52975 53016 53180 53260 53377 53396 53399 53690 53709 53903 53941 54591 54658 54728 54762 54851 54914 55063 55150 55165 55478 55520 55521 55685 55736 55744 56059 56359 56513 56692 57000 57073 57498 57521 57748 57830 58021 58396 58430 58496 58772 58832 59174 59439 59607 59860 59883 60307 60366 61281 61416 61421 61557 61600 61640 61668 62346 62359 62366 62605 62621 62866 63270 64200 64508 64699 64935 65034 65040 65141 65728 65870 65951 66018 66058 66323 66329 67153 67399 67525 67664 67868 67895 68402 68515 68652 68679 68813 69945 70103 70130 70204 70344 70350 70401 70597 70714 70755 70854 71217 71252 71559 71660 71862 71898 71944 72228 72295 72667 73092 73109 73182 73258 73387 73511 73526 73794 74589 74786 74815 75042 75397 75476 75599 75607 75931 75940 75943 76251 76571 76677 76683 77009 77244 77310 77353 77407 77489 77681 77833 77855 78182 78363 78590 78649 78722 78809 78835 79007 79177 79271 79744 79970 80182 80194 80656 81088 81350 81715 81791 81869 81949 81994 82069 82105 82207 82296 82434 82777 83063 83155 83317 83371 83729 84365 84585 84863 85808 86379 86458 86546 86715 86876 86963 87036 87671 87927 88170 88422 88487 88530 88586 89071 89113 89190 89553 89796 89821 90147 90290 90384 90801 91027 91181 91205 91551 91577 91648 91655 91660 92174 92331 92360 92380 92612 92655 92750 93146 93360 93458 93562 93687 93814 94133 94269 94487 94824 94854 95586 95606 95700 95767 95938 96332 96603 96707 96876 96885 97018 97272 97704 97718 97719 97969 98363 98469 98750 98928 99096 99131 99195 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. : 0.0361 s ( 0.05%) TIME: Pairwise Calc.: 0.3063 s ( 0.44%) TIME: Clustering : 0.2161 s ( 0.31%) TIME: Cluster Post. : 68.6172 s ( 99.19%) TIME: Total: 69.1757 s TIME: Analyses took 69.2008 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 : 2188.1135 s ( 96.93%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 69.2008 s ( 3.07%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2257.3145 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2284.1687 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.