CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:46:22 | Available memory: 66.302 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] 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 dme :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 DME (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] 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= 46.6609 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster dme :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 (137900000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 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: 11 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: 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 0.442631 #Cluster 1 has average-distance-to-centroid 0.667804 #Cluster 2 has average-distance-to-centroid 0.996963 #Cluster 3 has average-distance-to-centroid 0.941044 #Cluster 4 has average-distance-to-centroid 0.974571 #DBI: 1.400001 #pSF: 70442.068591 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 50477 74603 75616 89035 53924 #Sieve value: 200 (random) #Sieved frames: 808 1127 1155 1196 1505 1811 1955 2066 2170 2306 2494 2578 2620 2632 2679 3181 3495 3531 3941 5209 5323 5670 5772 6218 6266 6566 6760 7257 7522 7558 7561 7737 7764 8087 8364 8410 8424 9139 9828 10065 10494 10893 11798 12051 12123 12255 12316 12404 12752 12992 13421 13457 13843 14351 14864 15154 15229 15235 15273 15456 15457 15600 15652 15874 15993 16001 16251 16661 16671 16697 16945 17037 17133 17560 17774 18228 18254 18286 18459 19350 19547 20999 21494 21523 21657 21712 21766 22088 22244 22288 22436 22555 22665 22988 23334 23486 23519 23857 24173 24688 24776 24783 25027 25219 25305 25334 25761 26428 26575 26731 26848 27144 27167 27336 27651 27801 27809 27876 28092 28206 28351 28656 29089 29164 29620 30054 30079 30132 30619 30821 30824 31088 31322 31531 31868 32031 32397 32570 32702 32796 33065 33489 33581 33734 33764 33883 33887 33899 34185 34599 34604 34625 34826 34987 35583 35686 35807 35817 36044 36085 36609 36621 36627 36715 37046 37207 37404 37643 37676 38065 38070 38517 38745 38817 38826 38875 38995 39128 39540 39634 40462 40552 41552 41876 42109 42277 42632 42976 43142 43220 43265 43486 43695 44323 44671 44675 44707 44800 45139 45171 45349 45594 45912 45949 46146 46198 46651 46836 46985 47214 47256 47312 47320 47358 47842 48047 48054 48445 49012 49046 49392 49413 49649 49865 49911 49966 50091 50102 50131 50477 50792 51499 51652 51747 52014 52308 52771 52786 52944 52977 53141 53191 53476 53741 53899 53924 53943 54094 54295 55198 55296 55331 55663 55925 55927 56130 56157 56325 56845 57412 57954 58184 58351 58367 58686 58689 59117 59118 59268 59437 59852 60085 60302 60332 60674 60908 60994 61254 61334 61774 62302 62583 62622 62676 62719 62846 62930 63135 63263 63369 64037 64068 64352 64483 64499 64569 64578 64772 64793 65094 65258 66038 66521 66655 66695 67514 67550 67808 68316 68474 68501 68779 68957 68997 69221 69680 69863 70230 70270 70492 70627 70826 70839 70888 71207 71251 71444 71573 71943 72039 72370 72872 72929 72954 72958 73044 73376 73625 73662 73960 74603 75149 75198 75281 75579 75616 75623 76163 76323 76334 76464 76566 76603 77058 77301 77349 77459 77501 78239 78258 78561 78734 78822 78830 78841 78854 78991 79164 79335 79355 79621 79670 80033 80047 80376 80465 80546 80554 80587 80870 80920 80947 81228 81485 81538 81690 81695 81702 81738 81850 82364 82788 82848 83101 83395 83687 84027 84120 84176 84340 84446 84579 84635 84973 84987 85012 85112 85126 85608 85635 85740 85778 85829 86254 86312 86471 86630 87086 87261 87308 87478 87617 88021 88178 88184 88315 88475 88575 88936 88965 89035 89043 89126 89499 89688 89784 89791 90083 90163 90338 90400 90561 90729 90790 90833 90855 90868 90994 91221 91338 91661 91759 91902 92220 92594 92772 92909 92937 93039 93466 93634 94018 94198 94264 94318 94372 94433 94464 94481 94595 94832 95084 95112 95215 95271 95334 96047 96288 96473 96497 96729 96732 96895 96898 96953 97350 97536 97782 97796 97866 98088 98278 98344 98383 98563 98911 99111 99267 99665 99709 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. : 0.0122 s ( 0.02%) TIME: Pairwise Calc.: 0.1830 s ( 0.34%) TIME: Clustering : 0.0632 s ( 0.12%) TIME: Cluster Post. : 53.8340 s ( 99.52%) TIME: Total: 54.0924 s TIME: Analyses took 54.1171 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 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 2143.1217 s ( 97.54%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 54.1171 s ( 2.46%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2197.2389 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2220.6940 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.