CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 16:26:53 | Available memory: 15.980 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, 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= 86.0678 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. Loading pair-wise distances from CpptrajPairDist Warning: ClusterMatrix CpptrajPairDist contains sieved data. Loaded CpptrajPairDist: 100000 original rows, 500 actual rows, 124750 elements, sieve=-200 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: 8 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: 33 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 52 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 4 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 6 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 3 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 1 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 1.213947 #Cluster 1 has average-distance-to-centroid 1.360399 #Cluster 2 has average-distance-to-centroid 1.239475 #Cluster 3 has average-distance-to-centroid 1.795035 #Cluster 4 has average-distance-to-centroid 1.531648 #DBI: 1.469773 #pSF: 22309.268885 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 40313 77541 70674 59533 55878 #Sieve value: 200 (random) #Sieved frames: 65 138 243 788 874 899 1050 1191 1342 1374 1450 1681 1935 2028 2168 2260 2511 2556 2591 2645 2665 3522 3654 3950 3966 4220 4383 4598 4776 4779 4895 5399 5481 5706 6113 6247 6371 6934 7352 7411 7492 7562 7725 7941 8010 8070 8225 8351 8563 8583 8753 8829 9126 9285 9615 9733 10305 10383 10399 10472 10725 11036 11780 11911 12313 12335 12567 12855 13275 13316 13394 13614 13786 13816 13842 13958 13989 14183 14345 14561 14643 14826 15036 15354 15484 15760 15945 15978 16073 16323 16450 16474 16478 17270 17308 17560 17739 17989 18405 18420 19086 19412 20686 20964 20985 21290 21422 21935 21976 22038 22159 22320 22487 22573 22942 23098 23128 23165 23391 23636 23711 24066 24559 25008 25383 25678 25740 26330 26792 26897 27074 27096 27198 27321 28399 28497 28895 29020 29136 29335 29536 30057 30405 30490 31790 31962 32031 32429 32486 32760 33199 33603 33911 34068 34099 34238 34354 34411 34646 34792 34878 35127 36399 36666 37077 37215 37441 37554 37578 37617 37638 37773 38251 38579 38733 38761 38914 38993 39249 39367 39432 39570 39584 39585 39602 39880 40034 40074 40103 40313 40554 40730 40735 40839 40947 40974 41196 41606 41614 41679 41983 42107 42152 42191 42310 42339 42367 42372 43279 43539 43644 43965 44333 44524 44708 45075 45268 45565 46045 46164 46419 46442 46498 46880 47126 47261 47290 47406 47531 47619 47688 48016 48871 49351 49528 49544 49847 50256 50330 51011 51619 51837 52084 52314 52393 52537 52624 53348 53599 53707 53864 54360 54903 55057 55087 55103 55424 55557 55760 55793 55878 55960 56115 56331 56441 56700 56745 56790 56947 57176 57226 57407 58000 58352 58496 58639 59293 59423 59533 59565 59725 60207 60220 60550 60638 60748 61088 61145 61360 61379 61408 61706 61910 61959 62015 62176 62288 62589 63011 63359 63451 64341 64421 64475 64509 64588 65296 65540 65924 66032 66227 66338 66394 66475 66768 66846 67032 67213 67353 67898 67913 68044 68135 68262 68462 68982 69034 69142 69143 69239 69339 69349 69497 69561 69859 69963 69971 70042 70088 70496 70512 70592 70674 70738 70846 71067 71223 71260 71468 71545 72039 72176 72302 72608 72921 72975 73009 73130 73296 74062 74253 74493 74543 74603 74613 74709 74747 75153 75191 75497 75502 75889 76172 76187 76245 76376 76380 76542 76557 76799 76820 76869 77110 77183 77254 77541 77591 77648 77831 77906 77932 77964 78101 78213 78379 78462 78953 79132 80037 80055 80208 80238 80269 80749 81140 81416 81690 81863 81953 81990 82051 82481 82627 82693 82942 83062 83284 83312 83368 83565 83593 84170 84406 84495 85192 85302 85334 85566 85901 85932 86127 86270 86424 86541 87084 87532 87662 88181 88787 88829 89470 89562 89682 89725 89736 89799 89885 90367 90522 90878 90902 91028 91062 91506 92119 92460 92659 92781 92946 92994 93168 93349 93553 94176 94587 94705 94816 95010 95130 95252 95459 95710 95843 95853 95879 96332 96439 96587 96759 96794 96866 97000 97002 97019 97023 97144 97299 97339 97873 98208 98312 98458 98490 98580 98856 98879 98957 99503 99678 99949 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. : 0.0016 s ( 0.00%) TIME: Pairwise Calc.: 0.0340 s ( 0.06%) TIME: Clustering : 0.0837 s ( 0.14%) TIME: Cluster Post. : 60.2131 s ( 99.80%) TIME: Total: 60.3324 s TIME: Analyses took 60.3325 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 : 1161.8749 s ( 95.05%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 60.3325 s ( 4.94%) TIME: Data File Write : 0.1437 s ( 0.01%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 1222.3514 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1223.1833 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.