CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:37:06 | Available memory: 16.017 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 7 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 7 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= 24.8878 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 7 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 (150380000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 20% 30% 41% 51% 61% 71% 80% 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: 493 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 29 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 4 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: 7 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 1.031088 #Cluster 1 has average-distance-to-centroid 0.859399 #Cluster 2 has average-distance-to-centroid 1.363113 #Cluster 3 has average-distance-to-centroid 1.086560 #Cluster 4 has average-distance-to-centroid 1.614879 #Cluster 5 has average-distance-to-centroid 1.757721 #Cluster 6 has average-distance-to-centroid 1.587885 #DBI: 1.491184 #pSF: 21859.488725 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 73451 21025 26106 68371 81879 69076 72073 #Sieve value: 200 (random) #Sieved frames: 96 170 343 449 648 776 820 1488 1506 1622 1661 1748 1778 1804 1925 2096 2130 2343 2475 2678 2818 2979 3213 3407 3504 3781 3869 4024 4183 4203 4439 4598 4714 4898 5031 5051 5253 5378 5466 5797 5888 6213 6253 6313 6444 6660 7019 7112 7241 7519 7677 7722 7892 8055 8158 8164 8194 8257 8423 8513 8575 8721 8757 8804 9093 9136 9294 9964 10116 10127 10467 10801 10882 11030 11358 11595 12216 12790 13827 14052 14354 14483 14576 14777 14906 16001 16025 16723 16804 16905 17052 17117 17616 17730 18117 18297 18492 18712 18854 19182 19804 20074 20103 20238 20684 20712 21009 21025 21203 21319 21320 21526 22005 22081 22156 22311 22352 22444 22594 22596 22901 22960 23287 23351 23663 24243 24292 24360 24538 24729 24761 24901 25146 25299 25894 25986 26106 26129 26262 26294 26306 26835 26930 27130 27169 27874 28775 28782 28815 29139 29284 29787 30238 30355 30762 30931 30937 31182 31238 31250 31290 31502 31586 31893 32345 32594 32637 32980 33282 33337 33703 33910 34481 34641 34790 34792 35482 35842 35979 36080 36107 36263 36337 36636 36651 36987 37195 37433 37539 37640 37712 38351 38863 38883 39258 39507 39635 39908 40147 40224 40524 40592 40800 40834 41317 41459 41485 41563 41983 41994 42136 42285 42309 42315 42592 42918 43133 43262 43380 43488 43719 44008 44732 44782 44890 45328 45836 45881 46143 46220 46505 46573 47403 47448 47615 48196 49147 49517 49629 50184 50580 50780 50925 51154 51194 51230 51337 51410 51533 51975 52127 52375 52474 52941 53120 53274 53567 53656 53751 54086 54096 54336 54537 54729 55467 55640 55860 55861 55892 55903 55960 55970 56290 56409 56418 56647 56785 56854 56973 57220 57508 57726 58024 58296 58327 58555 58665 58951 59131 59241 60031 60665 60678 60713 60799 60841 61003 61338 61350 61517 61767 61848 62025 62145 62181 62293 62321 62343 62379 62435 62449 62654 62694 62933 62956 62967 63306 63523 63538 63960 64095 64374 64415 64426 65095 65562 65785 65868 66064 66087 66708 66863 67212 67241 67760 68098 68204 68371 68983 69076 69092 69224 69254 69308 69553 70119 70171 70607 70850 71106 72015 72052 72073 72148 72357 72455 72649 73042 73095 73142 73275 73451 73474 73640 74371 74474 74527 74822 74965 75066 75177 75261 75372 75802 75910 75913 76083 76214 76219 76271 76280 76422 76500 77026 77355 77402 77654 77716 77851 77926 78248 78506 78524 79066 79343 79912 80016 80215 80346 80551 80734 80817 80845 80955 81073 81127 81235 81547 81615 81879 82061 82202 82366 82664 82760 82840 82855 83381 83794 83952 84234 84332 84515 84641 84819 85249 85484 85602 85645 85776 85785 86006 86044 86366 86439 86609 86715 86845 86853 86889 87114 87164 87319 87365 87368 87644 87766 87888 88589 88880 88969 89042 89142 89319 89749 89866 90280 90348 90444 90738 90837 91604 91647 91785 91980 92111 92145 92154 92196 92635 92691 92789 93405 93650 93700 93899 93941 94719 95312 95335 95351 96017 96362 96941 97192 97315 97636 97964 98312 98881 98916 98927 99064 99084 99131 99419 99462 99494 99766 99782 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 'ctraj.c6' 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. Writing 'rep.c6.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.3302 s ( 0.56%) TIME: Pairwise Calc.: 0.1140 s ( 0.19%) TIME: Clustering : 0.0400 s ( 0.07%) TIME: Cluster Post. : 58.9214 s ( 99.18%) TIME: Total: 59.4056 s TIME: Analyses took 59.4057 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 : 4018.0408 s ( 98.54%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 59.4057 s ( 1.46%) TIME: Data File Write : 0.1360 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 4077.5826 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 4078.9435 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.