CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:54:02 | Available memory: 16.010 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, 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= 85.8013 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 (150970000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 21% 31% 40% 51% 61% 70% 81% 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: 26 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 5 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 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 0.585549 #Cluster 1 has average-distance-to-centroid 0.940548 #Cluster 2 has average-distance-to-centroid 0.871584 #Cluster 3 has average-distance-to-centroid 1.146080 #Cluster 4 has average-distance-to-centroid 1.099569 #DBI: 1.151947 #pSF: 42217.792474 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 28310 63166 99090 35441 7942 #Sieve value: 200 (random) #Sieved frames: 47 198 731 802 982 1102 1104 1175 1826 2015 2270 2328 3356 3730 4395 4434 4744 4757 4825 4863 4865 4866 5849 5877 6211 6549 6576 6662 6738 6749 6938 7007 7059 7367 7455 7593 7912 7942 8501 8791 9199 9433 9810 9904 10208 10691 10798 10812 10941 10976 11484 11585 11617 11802 12089 12126 12203 12281 12409 12742 13295 13363 14062 14113 14120 14450 14466 14758 14782 15029 15086 15290 15702 15985 16241 16262 16686 17172 17683 17717 17770 17788 17962 18116 18207 18335 18452 18685 18718 19031 19439 19591 19603 19701 20042 20844 20965 21290 21310 21429 21476 21554 21719 22059 22229 22498 22563 22635 22778 22988 22997 23031 23153 23342 23781 24212 24650 25170 25299 25740 25757 25910 26014 26054 26180 26234 26271 26340 27350 28267 28310 28441 28553 28574 28730 29333 29442 29518 29769 30086 30109 30760 30862 31226 31391 31407 31559 31573 31639 31919 32021 32083 32216 32311 32426 32488 32922 33021 33157 33188 33288 33363 33423 33687 33804 34071 34110 34223 34419 34504 35034 35083 35116 35160 35215 35250 35262 35441 35528 35534 35614 35830 36409 37087 37190 37574 37794 37902 38043 38157 38561 38843 38944 39057 39309 39424 39696 39707 39715 40771 41004 41185 41339 41720 41817 41890 42036 42140 42275 42692 42794 42837 43087 43178 43694 43854 43953 44114 44166 44199 44272 44312 44314 44399 44560 44752 45049 45107 45248 45406 45452 45588 46363 46519 46842 47333 47400 47459 47608 47687 47767 47870 48004 48574 48729 48747 48788 49166 49692 49785 50487 50920 51019 51279 51311 51320 51522 51736 52298 52517 52670 52928 53101 53252 53284 53604 53851 53898 53951 55014 55306 55371 55566 55704 55868 55953 56014 56110 56158 56342 56352 56547 56812 56820 57432 57460 57732 57824 57918 57968 57989 58619 59269 59400 59895 59959 60031 60151 60197 60225 60328 60466 60908 60959 61105 61121 61267 61293 61504 61574 61643 61920 61962 61988 62031 62086 62450 62706 62974 63166 63559 63626 64172 64206 64793 64859 65238 65263 65375 65379 65805 65972 65973 66117 66177 66368 66408 66824 67150 67771 68411 68597 69093 69215 69450 69607 69737 70066 70108 70185 70230 70280 70290 70296 70395 70843 71453 71514 71734 72057 72293 72354 72374 72573 73004 73043 73147 73167 73894 73921 73997 74129 74263 74467 74509 74551 74580 74666 74685 75231 75388 75537 75545 75634 75667 75874 75983 76119 76142 76215 76397 76428 76429 76618 76672 76814 76824 76993 77105 77333 77403 77439 78833 78854 78970 79073 79531 79589 79817 80116 80197 80318 80382 80669 80691 81080 81351 81643 81836 82055 82306 82443 82746 83218 83472 83629 83722 83798 83897 84270 84803 85321 85712 85810 86040 86226 86578 86597 86743 86889 86994 87260 87269 87473 87969 88358 88359 88536 88573 88765 88888 89211 89248 89277 89584 89652 89980 90191 90433 90628 90719 90894 90956 91211 91388 91440 91519 91529 92059 92079 92192 92378 92598 92641 92774 92780 92831 92864 93004 93061 93296 93310 93459 94603 94660 94945 95038 95136 95642 95792 96359 96384 96430 96596 96666 96854 97251 98597 99090 99278 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. : 0.3295 s ( 0.55%) TIME: Pairwise Calc.: 0.0929 s ( 0.16%) TIME: Clustering : 0.0213 s ( 0.04%) TIME: Cluster Post. : 59.0897 s ( 99.25%) TIME: Total: 59.5335 s TIME: Analyses took 59.5335 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 : 1165.4830 s ( 95.13%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.5335 s ( 4.86%) TIME: Data File Write : 0.1351 s ( 0.01%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 1225.1519 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1229.9568 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.