CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:36:14 | Available memory: 16.018 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 6 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 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, 3302 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: 66 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](42) Reference mask: [:1-2&!@H*](42) 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): 81.600 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= 25.1610 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 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] Starting clustering. Mask [:1,2&!@H*] corresponds to 42 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (150360000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 21% 31% 41% 51% 61% 71% 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: 494 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 13 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: 2 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 0.983996 #Cluster 1 has average-distance-to-centroid 0.976577 #Cluster 2 has average-distance-to-centroid 1.128907 #Cluster 3 has average-distance-to-centroid 1.490374 #Cluster 4 has average-distance-to-centroid 1.669978 #Cluster 5 has average-distance-to-centroid 1.916266 #DBI: 1.444660 #pSF: 27446.473446 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 62377 35638 38876 78816 29617 58871 #Sieve value: 200 (random) #Sieved frames: 605 711 761 1309 1799 2153 2346 2512 2777 2910 3008 3011 3259 3521 3540 3691 4243 4257 4302 4342 4734 4983 5007 5072 5522 5613 5625 5964 6051 6237 6275 6615 7348 7394 7671 7975 8053 8413 8595 8689 8906 9053 9120 9268 9407 9567 9782 9954 10466 10698 11002 11044 11209 11278 11452 12276 12476 12582 13035 13233 13502 13617 13829 13898 13902 13981 14358 14711 14746 14976 15586 16003 16049 16153 16261 16310 16786 16908 17145 17196 17303 17306 17530 17668 17763 18234 18356 18502 18507 18518 18593 18813 18891 18918 19145 19199 19299 19450 19778 19834 20037 20093 20240 20425 20491 21031 21376 21411 21949 22058 22286 22364 22645 22647 22714 22835 22995 22997 23129 23172 23477 23512 24217 24241 24318 24456 24460 25119 25844 25983 26250 26596 26616 26781 26954 27059 27242 27322 27633 28451 28457 28487 28780 29148 29183 29191 29198 29296 29349 29440 29598 29617 29719 29729 29752 29902 30741 30783 30955 31555 31714 32093 32163 32322 32342 32380 32529 32561 32904 33382 33956 33985 33996 34101 34414 34517 34757 34830 35638 36053 36174 36189 36241 36617 36700 36868 37214 37322 37458 37789 37852 37933 38443 38876 38913 39253 39610 39710 39793 39995 40077 40084 40392 40598 40731 40840 41021 41497 41623 41721 42170 42206 42611 42902 43092 43293 43451 43615 43751 44351 44561 44674 45118 45356 45574 46078 46183 46265 46596 46598 46732 46928 46984 47041 47151 47229 47410 47548 47813 47862 47906 48206 48317 48384 48596 48999 49076 49152 49207 49709 49811 49849 50452 50830 51289 52031 52100 52323 52724 52802 53414 53494 53594 53885 53983 54133 54421 55073 55322 55328 55528 55600 55601 55644 55657 56398 56495 56705 56970 56986 57357 57376 57602 57605 57659 57711 57736 57963 58020 58320 58373 58554 58670 58671 58871 59084 59530 60021 60318 60389 60422 60511 60635 61836 61854 61877 61917 62299 62317 62377 62968 63019 63047 63108 63255 63388 63503 63662 63979 63987 64064 64495 64620 64625 65180 65312 65331 65518 65708 65842 66211 66887 67164 67190 67401 68082 68886 69036 69222 69447 69554 69745 70081 70110 70168 70450 70467 70480 70659 70773 71970 72312 72396 72431 72442 72490 72508 72717 72903 73016 73049 73051 73076 73252 73606 73776 74444 74568 74640 74646 75051 75774 75820 75906 76206 77328 77602 77972 78037 78336 78816 78920 78933 79014 79042 79089 79224 79295 79761 80163 80231 80244 81536 81891 81893 81985 82303 82595 82825 82881 83070 83104 83131 83254 83375 83901 84183 84367 84375 84527 84643 84654 84668 84764 84955 84964 85024 85418 86136 86359 86697 86721 86775 86956 87146 87254 87299 87391 87582 87762 87785 88018 88250 88407 88464 88708 88754 88978 89276 89413 89452 89612 89695 90293 90352 90427 90707 91286 91588 91614 91778 91897 92053 92472 92473 92496 92781 92889 93074 93132 93175 93206 93570 93817 93819 93915 94221 94408 94623 94791 94799 95146 95257 95298 95605 95701 96229 96283 96312 96424 96459 96679 96774 96784 96878 97004 97594 97727 97782 98225 98292 98324 98612 98753 99067 99182 99439 99562 99680 99863 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. : 0.3557 s ( 0.60%) TIME: Pairwise Calc.: 0.0735 s ( 0.12%) TIME: Clustering : 0.0449 s ( 0.08%) TIME: Cluster Post. : 59.1301 s ( 99.20%) TIME: Total: 59.6043 s TIME: Analyses took 59.6043 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (81.600 MB) Box Coords, 66 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 : 3974.3985 s ( 98.52%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.6043 s ( 1.48%) TIME: Data File Write : 0.1375 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 4034.1405 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 4041.6059 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.