CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 16:28:26 | Available memory: 15.984 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, 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= 86.3098 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 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (149500000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 21% 30% 40% 51% 61% 71% 82% 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: 16 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 3 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 1 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: 5 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.792276 #Cluster 1 has average-distance-to-centroid 1.553174 #Cluster 2 has average-distance-to-centroid 1.362724 #Cluster 3 has average-distance-to-centroid 1.166271 #Cluster 4 has average-distance-to-centroid 1.636394 #DBI: 1.338787 #pSF: 40733.507495 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 89650 65694 64515 14249 3322 #Sieve value: 200 (random) #Sieved frames: 199 475 507 548 572 665 807 1214 1292 1299 1781 1922 2368 2399 2555 2711 2820 2936 3322 3627 3869 4204 4262 4375 4444 4536 4561 4706 5130 5715 5758 6546 6554 6640 6934 7049 7057 7451 7816 7963 8321 8401 8914 9004 9053 9760 9783 9890 10006 10190 10283 10526 10574 10829 11232 11415 11730 12158 12168 12185 12526 12631 13195 13204 13316 13333 13547 13561 13770 13866 13869 14249 14286 14428 14481 14492 14877 14911 15534 15660 16387 17226 17258 17271 17508 17509 17592 17599 17771 17876 18029 18137 18309 18348 18450 18577 18830 18831 19104 19686 19881 19924 19926 20300 20321 20328 20434 20759 20801 20814 20876 20929 21024 21226 21280 21449 21471 21524 21910 21987 22052 22376 22404 22725 22987 23703 23973 24308 24374 24377 24471 24752 24817 24942 25133 25193 25353 25407 26351 26476 26517 26590 26614 27396 27699 27778 27790 28015 28051 28113 28197 28228 28241 28410 28606 28614 28721 28814 28824 29086 29114 29131 29155 29196 29319 29460 29554 29804 29822 29922 30199 30532 30841 31319 31382 31402 31419 31439 31460 31604 32017 32093 32736 33205 33260 33798 34377 34595 34756 34906 34971 35712 35847 36199 36312 36343 36708 36857 37000 37116 37451 38138 38254 38740 38836 39257 39371 39443 39742 39902 39988 40228 40248 40457 40466 40480 40511 40641 40780 40802 41043 41130 41212 41374 41593 42023 42107 42584 42965 43010 43012 43468 43603 43637 43912 43945 44101 44572 44741 44767 44840 45216 45784 45976 46185 46276 46549 46592 47079 47116 47193 47333 47343 47381 47469 47843 47858 48151 48778 49130 49220 49382 50005 50392 50413 50511 50745 50827 51086 51348 51664 51696 51722 51847 51850 52223 52394 52804 54248 54603 54977 55001 55203 55304 55454 55644 55816 55896 56187 56236 56279 56847 57086 57296 57522 57666 57747 57841 57980 58196 58301 58310 58468 58624 58780 59155 60083 60183 60461 60559 60658 60666 61124 61453 61833 62501 62889 63354 63640 63921 63941 64515 64560 64670 64928 65377 65653 65694 65733 65776 66285 66462 66575 67350 67601 67662 67894 68401 68476 68543 68759 68916 69042 69074 69096 69141 69418 69840 69900 69977 70091 70235 70518 70554 70778 70930 70948 70960 71002 71093 71339 71604 71889 72018 72623 72856 73109 74648 74756 74845 75437 75499 75785 75888 76019 76294 76311 76411 76453 76627 76652 76998 77519 77688 78137 78291 78729 78870 79257 79387 79440 79536 79606 79654 79841 79864 79902 80211 80305 80480 80834 81215 81375 82232 82298 82756 82853 82869 82903 82976 83203 83370 83395 83533 83661 84009 84061 84195 84476 84949 85170 85449 85601 85771 85822 86291 86473 86639 86866 87002 87217 87327 87645 87688 87700 87934 88148 88186 88463 88543 88578 88855 89277 89302 89455 89563 89650 89680 89767 90074 90284 90715 90833 90922 90984 91121 91234 91344 91375 91839 92308 92328 92453 92617 92672 92998 93327 93449 93647 93659 93757 94022 94258 94282 94765 94808 95015 95410 95573 95605 95666 95863 95953 95963 96188 96330 96721 97182 97317 97364 97382 98460 98519 98617 99248 99305 99363 99571 99665 99827 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. : 0.3219 s ( 0.53%) TIME: Pairwise Calc.: 0.0514 s ( 0.08%) TIME: Clustering : 0.0382 s ( 0.06%) TIME: Cluster Post. : 60.1227 s ( 99.32%) TIME: Total: 60.5342 s TIME: Analyses took 60.5342 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 : 1158.6166 s ( 95.02%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 60.5342 s ( 4.96%) TIME: Data File Write : 0.1351 s ( 0.01%) TIME: Other : 0.0002 s ( 0.00%) TIME: Run Total 1219.2862 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1223.5153 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.