CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:38:16 | Available memory: 15.681 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&!@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 RMSD (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, 3299 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: 63 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): 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= 75.1411 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 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] Starting clustering. Mask [:1,2&!@H*] corresponds to 40 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (188710000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 11% 21% 30% 40% 51% 61% 70% 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: 3 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% 60% 70% 80% 90% Complete. #Clustering: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.588478 #Cluster 1 has average-distance-to-centroid 1.359884 #Cluster 2 has average-distance-to-centroid 0.791546 #Cluster 3 has average-distance-to-centroid 1.738828 #Cluster 4 has average-distance-to-centroid 1.716358 #DBI: 1.219012 #pSF: 37046.194411 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 47928 37235 29303 49959 59368 #Sieve value: 200 (random) #Sieved frames: 147 253 1032 1057 1178 1414 1514 1706 1905 2068 2438 2653 2835 2843 2902 2905 2944 3304 3540 3619 3899 4089 4116 4185 4226 4962 5015 5266 5449 5656 5780 5879 6498 6586 7034 7244 7313 7670 8127 8136 8256 8387 8525 8528 8938 9293 9398 9429 9518 9699 9961 10183 10358 10410 10658 10753 10945 11460 11776 11821 12067 12069 12127 12314 12536 12585 12764 12779 12860 13073 13205 13481 13727 13773 13780 14293 14298 14434 14553 14644 15044 15318 15643 15951 16312 16359 16550 17022 17038 17196 17332 17381 17673 18124 18471 18539 18559 18740 18880 18969 19001 19475 19794 19874 19940 20296 20414 20574 21072 21138 21426 21715 21756 22417 22807 22860 23050 23150 23351 23854 23859 23869 24046 24078 24252 24505 24929 25307 26195 26199 26324 26545 26546 26697 26981 27180 27364 27495 27646 28474 28689 28972 29041 29303 29385 29645 29699 29807 30013 30022 30050 30064 30114 30514 30638 30788 30986 31022 31506 31642 31661 31853 31985 32175 32342 32438 32598 32834 32939 33047 33192 33402 33572 33784 34014 34267 34452 34549 34577 34650 34764 34924 35073 35463 35750 35897 36072 36121 36266 36602 36830 36925 37129 37235 37445 37502 37515 37624 37796 37814 37843 37953 38161 38289 38645 39432 39460 39533 39904 40587 40780 41173 41349 41636 41920 42026 42195 42421 42570 43873 44154 44247 44418 44457 44483 44808 44821 45280 45438 45514 45656 45762 46674 46958 47071 47485 47830 47856 47928 48310 48382 48434 48757 48955 48968 49910 49959 50187 50209 50314 50339 50392 50761 50999 51202 51207 51874 51968 52061 52103 52333 52481 52709 52936 53117 53268 53556 53558 53617 53634 53857 53895 54124 54181 54232 54443 54632 54711 54725 54964 54973 55005 55202 55298 55322 55940 55958 56182 56652 56901 57067 57275 57485 57559 57692 57720 58029 58512 59019 59039 59272 59277 59368 59465 59692 59876 59919 60218 60840 61143 61192 61196 61409 61911 62008 62041 62397 62415 62593 62706 62820 63989 64047 64187 64463 64536 64575 64593 64600 65717 66216 66273 66342 66430 66537 66602 66705 66750 66873 67176 67691 67838 67959 67965 68204 68327 68470 68538 68571 68640 68937 68954 69003 69127 69827 69941 70061 70439 70468 70793 70826 71254 71686 71809 71837 71893 72445 72760 73056 73088 73533 73567 73734 73859 74033 74231 74310 74529 74844 75039 75298 75507 76040 76059 76178 76264 76638 76671 76725 76989 77326 77463 77530 77623 77642 78344 78574 79275 79551 79591 79677 79728 79809 79949 80059 80219 80317 80327 80419 80443 80663 81686 81828 81985 82250 82436 82553 82692 83065 83401 83725 83848 83857 84076 84167 84697 84723 84863 85227 85734 86405 86716 86744 86845 87300 87306 87330 87505 87610 87671 88026 88159 88215 88413 88536 88638 89426 89449 89731 89785 89924 90115 90162 90405 90479 90482 90570 90577 90743 90780 90861 91652 91704 91899 92191 92459 92486 92883 93051 93370 93412 93543 93580 93768 93923 93950 94554 94645 95144 95265 95367 95684 95839 96154 96251 96377 96803 96830 97439 97568 98391 98461 98570 98887 98919 99261 99336 99831 99910 99948 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. : 0.3251 s ( 0.44%) TIME: Pairwise Calc.: 0.0983 s ( 0.13%) TIME: Clustering : 0.1069 s ( 0.14%) TIME: Cluster Post. : 73.4823 s ( 99.28%) TIME: Total: 74.0126 s TIME: Analyses took 74.0126 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 DATAFILES (1 total): test.dat (Standard Data File): RMSD_00001 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1330.8287 s ( 94.72%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 74.0126 s ( 5.27%) TIME: Data File Write : 0.1634 s ( 0.01%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 1405.0052 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1411.4867 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.