CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:55:44 | Available memory: 16.001 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@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2]) 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, 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= 86.0640 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2] corresponds to 11 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (152030000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 11% 20% 31% 40% 51% 62% 71% 81% 90% 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: 27 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 21 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 22 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 11 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 3 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 1 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 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 0.618770 #Cluster 1 has average-distance-to-centroid 0.971192 #Cluster 2 has average-distance-to-centroid 0.774294 #Cluster 3 has average-distance-to-centroid 0.720464 #Cluster 4 has average-distance-to-centroid 0.865288 #Cluster 5 has average-distance-to-centroid 0.862254 #Cluster 6 has average-distance-to-centroid 1.053115 #DBI: 1.046777 #pSF: 36847.169075 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 45624 6073 7223 30601 31990 35518 16606 #Sieve value: 200 (random) #Sieved frames: 251 465 521 1349 1368 1693 1739 1961 2001 2076 2193 2289 2630 2636 2938 3103 3284 3553 3726 3789 4109 4138 4300 4572 4834 4874 4876 4923 5244 5644 5685 5994 6073 6074 6152 6647 6760 6985 7196 7204 7223 8002 8406 8410 8649 8884 9048 9346 10009 10341 10584 10984 10993 11011 11364 11376 11411 11482 11689 11713 11990 12510 12759 13138 13514 13717 14001 14144 14839 14972 15032 15052 15065 15176 15199 15660 15682 15712 15802 15949 16122 16606 16642 16860 17219 17411 17420 17522 17747 17900 18336 18553 18675 18781 19046 19129 19195 19353 19549 19626 19732 19823 19931 20339 20352 20723 20843 20948 21269 21788 21838 21914 22171 22193 22194 22278 22612 22722 22845 23284 23338 23343 23388 23577 23869 23927 24090 24113 24230 24252 24389 24837 25240 25311 25380 25533 25936 25991 26007 26059 26182 26412 26927 26955 26984 27254 27490 27656 27852 27963 28225 28346 28578 28755 28862 29148 29489 30055 30277 30601 30984 31077 31098 31121 31862 31894 31990 32144 32188 32409 32705 33240 33247 33525 33531 33722 34143 34622 35277 35518 35640 36004 36033 36195 36211 36792 36847 36961 36990 37187 37638 37779 37795 38468 38532 39190 39265 39511 39652 39925 40134 40305 40395 40809 40931 40943 40945 41996 42126 42145 42239 42454 42563 42655 42676 42685 42801 43193 43451 43889 44124 44324 44800 45439 45624 45800 45821 45845 45866 46036 46165 46244 46319 46942 47222 47315 47640 47686 47801 47839 48371 48405 48464 48588 48696 48748 48788 48861 48944 49048 49192 50027 50032 50150 50346 50434 50827 51037 51244 52557 52707 53069 53195 53284 53392 53759 54119 54161 54203 54297 54478 54489 54599 55068 55217 55758 55876 56102 56340 56345 56365 56548 56707 56720 56777 56926 57029 57046 57136 57737 57830 58110 58340 58721 58848 58998 59272 59613 59835 59878 60299 60651 60990 61016 61164 61209 61212 61693 61742 62381 62528 62657 62920 62979 63382 63695 63870 64124 64157 64385 64398 64739 64945 65320 65338 65497 65630 65697 65789 65870 65915 66052 66566 66667 66828 66883 66960 67243 67794 67983 68060 68415 68524 68608 69058 69209 69240 69319 69588 69591 69722 69939 69940 69980 70413 70534 70603 70899 71023 71097 71382 71414 71556 71621 72286 72406 72420 72431 72776 72981 72994 72997 73522 73939 74042 74119 74127 74481 74568 74919 74927 75264 75417 75423 75478 75855 76000 76245 76497 76636 76881 76905 77270 77273 77654 77769 77931 78467 78687 79030 79042 79080 79142 79346 79479 79724 80252 80560 80573 80592 80857 81757 81790 81936 81955 82354 82622 82902 83017 83034 83140 83148 83409 83701 83727 83886 84009 84214 84494 84677 84872 84906 85120 85671 85886 86078 86220 86827 87022 87578 87596 87855 88425 88438 88570 88721 88915 88926 89424 89467 89474 89501 90908 91013 91830 91842 91903 92118 92277 92404 92701 92718 92949 93311 93375 93434 93767 93887 94289 94342 94370 94475 94627 94875 95020 95394 95437 95462 95740 95977 96403 96419 96455 96781 96787 96935 97309 97321 97476 97891 98582 98701 98835 99090 99206 99306 99534 99573 99580 99624 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. : 0.3246 s ( 0.57%) TIME: Pairwise Calc.: 0.0421 s ( 0.07%) TIME: Clustering : 0.0513 s ( 0.09%) TIME: Cluster Post. : 56.3228 s ( 99.26%) TIME: Total: 56.7408 s TIME: Analyses took 56.7409 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 : 1161.9266 s ( 95.33%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 56.7409 s ( 4.66%) TIME: Data File Write : 0.1337 s ( 0.01%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1218.8013 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1219.6425 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.