CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:40:15 | Available memory: 16.016 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, 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= 25.6343 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 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (148090000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 10% 20% 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: 11 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 1 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: 6 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.943214 #Cluster 1 has average-distance-to-centroid 1.399944 #Cluster 2 has average-distance-to-centroid 1.285893 #Cluster 3 has average-distance-to-centroid 1.299144 #Cluster 4 has average-distance-to-centroid 1.356282 #Cluster 5 has average-distance-to-centroid 1.627854 #DBI: 1.400786 #pSF: 32204.368478 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 52075 76586 55067 62718 81598 78039 #Sieve value: 200 (random) #Sieved frames: 51 119 435 616 768 1015 1310 1628 1993 2262 2277 2332 2680 3227 3424 3738 3853 3879 3883 3952 3974 3982 4215 4594 4623 4858 5816 5849 6175 6541 6716 6758 6854 7237 7398 7667 7755 7808 7960 8319 8461 8581 8696 9200 9212 9343 9453 9713 9750 10013 10158 10361 10431 10607 10820 10827 10936 11422 11442 11854 12098 12222 12362 12403 12714 12785 12799 13397 13406 13675 13975 14180 14322 14358 14432 14436 14719 14756 15182 15433 15767 15918 16296 16304 16322 16410 16480 16564 16691 16713 16921 16951 17504 17732 17982 18238 18304 18320 18379 18660 18719 18725 19403 19942 19999 20068 20215 20284 20482 20490 20725 20890 21397 21478 21546 21553 21565 21609 21890 22106 22564 22708 22902 22929 22984 23003 23452 23499 23708 24193 24498 24678 24684 24712 24950 25220 25761 25773 26084 26269 26466 26648 26830 27356 27377 27681 27781 27915 28255 28958 29548 29587 29949 30009 30241 30326 30363 30693 30719 30957 31211 31590 31611 31643 31669 31910 32445 32474 32755 32972 32998 33123 33133 33152 33716 33772 34045 34426 34655 34871 34924 35163 35205 35256 35601 35974 36282 36567 37011 37087 37148 37156 37319 37538 37578 37594 37661 37698 38787 38839 39105 39191 39233 39504 39861 40292 40533 40589 40624 40797 40921 41009 41221 41561 41588 41797 41805 41841 42236 42381 42399 42567 42670 43439 43596 43652 43701 43968 44021 44069 44209 44333 44482 44497 44536 44576 44618 44677 44682 44935 45258 45419 45670 46081 46155 46252 46724 46912 47107 47354 47532 47591 47639 47647 47735 47907 48121 48195 48251 48254 48384 48535 48595 48887 49484 49772 50091 50143 50889 51011 51305 51687 51908 52075 52567 52833 53335 53366 53646 53652 54228 54336 54742 55067 55615 55677 55687 56601 56685 57624 58501 58509 58531 58560 58596 58874 59026 59126 59284 59288 59307 59965 60198 60220 60242 60323 60408 60482 60506 60732 60957 61230 61506 61819 61897 62181 62403 62520 62718 62879 62897 63312 63560 63883 64104 64152 64518 65104 65315 65353 65378 65388 65511 66012 66021 66035 66189 66340 66749 66926 67288 67511 67724 68053 68070 69247 69537 69602 70461 70588 70692 70749 70786 70788 70798 70963 71145 71173 71389 71488 71676 71890 72086 72140 72180 73100 73231 73596 73999 74135 74276 74364 74764 75186 75324 75342 75447 76093 76135 76452 76586 76720 77100 77224 77344 77475 77949 77960 78039 78216 78831 78918 79033 79321 79687 79698 79933 80180 80407 80905 81110 81306 81383 81496 81598 81934 81938 81993 82096 82817 82925 82987 83178 83348 83737 84001 84146 84405 84493 85142 85282 85319 85470 85739 85793 85860 86128 86400 86493 86522 87170 87292 87514 88026 88203 88308 88446 88996 89285 89289 89358 89547 89600 89671 90113 90150 90192 90321 90350 90609 90681 90795 91324 91511 91563 91607 91608 92003 92257 92333 92381 92628 92767 93735 93949 94262 94271 94559 94676 94975 95108 95146 95192 95199 95335 95445 95567 95645 95850 95920 96126 96287 96523 96737 96746 97050 97084 97545 97614 97824 98099 98788 98872 99182 99444 99534 99618 99731 99803 99997 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. : 0.3279 s ( 0.56%) TIME: Pairwise Calc.: 0.0659 s ( 0.11%) TIME: Clustering : 0.0354 s ( 0.06%) TIME: Cluster Post. : 57.9835 s ( 99.27%) TIME: Total: 58.4127 s TIME: Analyses took 58.4128 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 : 3901.0198 s ( 98.52%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 58.4128 s ( 1.48%) TIME: Data File Write : 0.1366 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 3959.5693 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3963.2436 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.