CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 16:26:17 | Available memory: 15.978 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, 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= 86.0381 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 42 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (190170000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 1% 10% 21% 31% 41% 51% 61% 70% 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: 495 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 75 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 10 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 1.005850 #Cluster 1 has average-distance-to-centroid 0.945936 #Cluster 2 has average-distance-to-centroid 1.196581 #Cluster 3 has average-distance-to-centroid 1.452823 #Cluster 4 has average-distance-to-centroid 1.995189 #DBI: 1.286129 #pSF: 32491.712170 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 94510 52722 74 47710 35114 #Sieve value: 200 (random) #Sieved frames: 74 199 298 333 551 773 926 1107 1169 1691 1758 1796 2083 2193 2286 2331 2489 2575 2635 2700 2762 2810 2826 3029 3207 3458 3584 4073 4098 4182 4301 4358 4889 5587 5662 5766 5874 5909 6101 6606 6668 6857 6878 6954 7473 7580 8003 8249 8458 8700 8775 8803 9010 9185 9437 9511 9524 9837 9865 10179 10266 10426 10638 10768 10835 11126 11130 11469 12933 13427 14417 14725 15308 15392 15519 15888 15900 15940 16401 16540 16606 16948 17035 17460 17517 17717 17767 17899 18091 18947 18953 19246 19510 19542 19843 19883 20864 21096 21368 21521 21554 21799 21980 22122 22226 22405 22799 23046 23339 23364 23503 23578 23599 24151 24516 24858 24912 24959 25072 25193 25538 25900 26284 26294 26429 26444 26730 26850 26914 26972 27072 27159 27216 27249 27604 27933 29151 29270 30045 30247 30293 30323 30646 31344 31490 31513 32115 32609 32725 32792 33247 33263 33665 34040 34191 34192 34235 34627 34885 35097 35114 35280 35509 35579 35704 35817 36249 36328 36415 36507 36651 36691 36725 36946 37082 37401 37434 37603 37640 37696 37766 37778 37807 37864 38153 38866 39114 39334 39603 39931 40103 40173 40428 40681 40880 41152 41153 41244 41468 41691 41821 42276 42384 42414 42560 42567 42690 43390 43421 43532 43578 43861 44156 44522 44530 44817 44858 45125 45153 45239 45328 45366 45382 45988 46024 46034 46226 46477 46662 46855 47315 47326 47530 47570 47710 47774 48084 48329 48557 48796 49132 49310 49367 49537 49844 50092 50512 50556 50662 50956 51457 51834 52445 52651 52722 52773 53012 53078 53279 53470 53486 53855 54002 54067 54162 54393 54660 54891 54960 54998 55681 56285 56462 56568 56652 56791 56878 57068 57472 57819 57921 57935 57960 58090 58560 58714 59089 59101 59655 59744 59875 60144 60146 60182 60269 60292 60492 60579 60679 60741 61139 61200 61290 61598 61710 61882 61910 62997 63099 63538 63728 63914 64375 64511 64809 64917 65123 65190 65572 65887 65907 66121 66184 66853 66884 66928 66965 67303 67362 67374 67405 67491 67794 67867 67932 68460 68523 68560 68858 68929 68985 69165 69339 69452 69835 70038 70439 70669 70760 71008 71068 71194 71300 71302 71403 71881 71965 71969 72044 72057 72342 72373 72504 72605 73034 73332 73336 73490 73773 74009 74737 74752 74780 74931 75225 75233 75328 75482 75577 75691 75747 75827 75999 76080 76298 76658 76887 77171 77308 77373 77421 77440 77858 78074 78270 78698 78781 78852 79033 79178 79329 79475 79731 79765 79947 80117 80204 80409 80539 80547 80709 80771 80825 80932 80989 81098 81451 81756 81857 82307 82788 82847 83248 83773 83986 83994 84062 84087 84144 84290 84387 84970 85126 85760 85888 85911 85955 85989 85997 85999 86300 86776 87222 87224 87422 87425 87700 88195 88254 88451 88525 88654 88797 89102 89493 89498 89739 89788 90428 90659 90835 91478 91966 92099 92378 92491 92587 92660 92691 92880 92889 93178 93268 93681 93808 93853 94466 94510 94919 95232 95274 95325 95377 95982 96324 96581 96870 96896 96927 97086 97389 97670 98359 98691 98928 98932 99445 99728 99755 99813 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. : 0.4339 s ( 0.59%) TIME: Pairwise Calc.: 0.0724 s ( 0.10%) TIME: Clustering : 0.0594 s ( 0.08%) TIME: Cluster Post. : 73.0094 s ( 99.23%) TIME: Total: 73.5752 s TIME: Analyses took 73.5752 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 : 1162.2759 s ( 94.03%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 73.5752 s ( 5.95%) TIME: Data File Write : 0.1621 s ( 0.01%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1236.0134 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1239.4313 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.