CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 17:33:10 | Available memory: 66.005 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, 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 out test.dat] 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= 50.3970 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 (140490000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 11% 21% 31% 41% 50% 60% 71% 80% 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: 14 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 10 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% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 6 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.592279 #Cluster 1 has average-distance-to-centroid 0.906093 #Cluster 2 has average-distance-to-centroid 0.817874 #Cluster 3 has average-distance-to-centroid 0.751961 #Cluster 4 has average-distance-to-centroid 1.024836 #Cluster 5 has average-distance-to-centroid 1.151191 #DBI: 1.054479 #pSF: 41037.095109 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 20530 15958 50479 19474 94095 7726 #Sieve value: 200 (random) #Sieved frames: 13 401 430 505 786 845 1050 1208 1644 1704 1878 1937 1998 2093 2121 2228 2434 2718 2847 2925 2952 3031 3057 3397 3480 3880 4222 4409 4746 4878 4920 5112 5211 5301 5601 5649 5702 5974 6204 6306 6521 6701 6714 7087 7110 7220 7251 7598 7726 7953 8325 8455 8678 9236 9382 9465 9500 9652 9940 10103 10142 10381 11174 11383 11586 11729 11916 11967 12826 12888 13144 13467 13471 13726 14797 14844 15249 15380 15448 15735 15830 15958 16215 16269 16363 16443 16463 16916 17171 17318 17811 17836 18111 18157 18207 18274 18432 18433 18623 18657 18708 18788 18824 19027 19194 19342 19388 19474 19564 19700 20376 20473 20530 20635 20981 21121 21197 21354 21706 21883 22178 22350 22371 22504 22782 22863 23229 23733 24056 24180 24227 24392 24861 24899 25327 25329 25366 25407 25414 25496 25704 25993 26460 26620 26686 27082 27427 27713 28136 28257 28548 28601 29524 29802 29987 30122 30224 30311 30334 30341 30392 30922 31099 31135 31172 31344 31371 31393 31438 31460 31532 31643 31779 32518 32526 32767 32783 32809 33474 33833 33851 35259 35472 35658 35663 35722 35816 36154 36582 36682 36925 36970 37031 37410 37674 37962 37967 38344 38367 38519 38949 39111 39574 40151 40199 40343 40900 41147 41229 41301 41351 41799 42207 42338 42418 42695 42696 43650 43693 43740 43962 43966 44017 44080 44106 44170 44797 44943 44961 45157 45175 45348 45909 45981 46220 46230 46240 46286 46444 46627 46676 46816 46832 46943 47298 47342 47347 47425 47483 47517 48074 48175 48213 48226 48243 48265 48833 49081 49371 49402 50055 50127 50385 50479 50504 50618 50644 50814 51162 52219 52358 52616 52844 52848 53237 53885 53930 53937 53938 54319 54428 54480 54566 55063 55302 55339 55387 55476 55649 55653 56798 56858 56913 57128 57289 57555 57778 57895 57948 58502 58581 58980 59186 59477 59657 59671 59854 60032 60093 60188 60295 60511 60634 60799 60872 60949 61244 61767 61773 62112 62211 62338 62429 62607 62853 63101 63198 63247 63546 63816 64279 64293 64339 64456 64861 64934 65035 65062 65233 65337 65398 65504 65606 66057 66206 66642 67845 68053 68067 68562 69318 69401 69406 69457 69667 69946 70117 70172 70407 70521 70708 70766 71050 71200 71551 71623 71672 71789 72147 72369 72430 72470 72537 72679 72722 72765 72943 73213 73216 73519 73891 73927 73933 74118 74380 74385 74416 74518 74949 75063 75384 75460 75507 75753 75867 76719 76950 77042 77063 77407 77410 78034 78352 78627 78718 78856 79030 79126 79340 79686 79920 80300 80529 80670 80868 81276 81997 82013 82179 82637 82789 82834 82875 82963 83187 83223 83270 83469 83836 83948 83964 84310 84450 84800 84911 86399 86717 86817 87193 87281 87545 87753 87796 87825 88028 88123 88131 88268 88274 88285 88360 88367 88428 88755 88837 89263 89412 89563 89564 89648 89649 90242 90427 90448 90991 91876 92131 92720 92848 92906 93244 93308 93591 94095 94332 94711 95016 95019 95311 95335 95570 95693 96256 96503 96652 96922 97201 97438 97524 97561 97669 97699 97729 97900 97945 98414 98511 99386 99593 99837 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. : 0.0265 s ( 0.04%) TIME: Pairwise Calc.: 0.0465 s ( 0.06%) TIME: Clustering : 0.0278 s ( 0.04%) TIME: Cluster Post. : 71.5610 s ( 99.86%) TIME: Total: 71.6618 s TIME: Analyses took 71.6860 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 DATAFILES (1 total): test.dat (Standard Data File): RMSD_00001 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1984.2444 s ( 96.51%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 71.6860 s ( 3.49%) TIME: Data File Write : 0.1526 s ( 0.01%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2056.0832 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2062.7445 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.