CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 13:14:48 | Available memory: 15.999 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, 3299 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: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](40) Reference mask: [:1-2&!@H*](40) 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): 78.000 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= 74.8889 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 40 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (188180000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 20% 31% 41% 52% 62% 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: 51 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 2 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 0.716900 #Cluster 1 has average-distance-to-centroid 1.009167 #Cluster 2 has average-distance-to-centroid 1.069366 #Cluster 3 has average-distance-to-centroid 1.708646 #Cluster 4 has average-distance-to-centroid 1.431843 #Cluster 5 has average-distance-to-centroid 1.526186 #DBI: 1.321872 #pSF: 36372.782722 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 72649 41325 19051 32733 20837 10989 #Sieve value: 200 (random) #Sieved frames: 23 102 621 1042 1768 1881 1922 2395 2475 2535 2659 3170 3356 3566 3642 4325 4332 4398 4541 4573 4699 5057 5116 5169 5214 5218 5836 5928 6044 6069 6165 6587 6688 6709 6838 6923 6995 7360 7955 8186 8484 8603 8884 9122 9612 9707 10104 10194 10699 10989 11391 11425 11931 12145 12284 12355 12624 13019 13697 13805 14328 14826 15047 15078 15173 15331 15400 15578 15831 15986 16126 16276 16679 17138 17245 17999 18317 19051 19140 19244 19319 19398 19566 19638 19718 19766 20460 20837 20903 20940 20958 21007 21262 21568 21726 21867 22054 22107 22352 22480 22686 22705 22841 22949 22963 23115 23329 23376 23740 24980 25039 25191 25285 25612 26386 26530 26550 26639 26650 27204 27317 27352 27405 27554 28405 28445 28746 28758 28823 29015 29507 29712 29852 29892 30397 30760 31005 31218 31256 31514 31542 31753 31799 31933 32054 32111 32191 32198 32248 32258 32297 32402 32486 32647 32720 32733 32876 32929 33077 33258 33341 33566 33964 34473 34939 35087 35604 35793 36222 36738 36786 36825 36827 36885 36960 37086 37718 37822 37965 38074 38199 38460 38941 39087 39122 39192 39234 39388 40445 40549 40629 40891 40916 40970 41128 41131 41325 41636 41738 41792 41909 42120 42319 42361 42384 42404 42914 43379 43598 43734 43951 44197 44435 44536 44649 44938 45181 45456 45500 45546 46155 46188 46218 47314 47431 47675 47793 48110 48240 48339 48595 48609 48990 49002 49038 49595 49670 50583 50819 51204 51343 51580 51698 51904 52004 52228 52293 52322 52640 53093 53580 53654 53840 54045 54102 54182 54278 54872 55393 55433 55622 55636 56012 56150 56248 56257 56848 56924 56945 57018 57175 57205 57222 57247 57248 57487 57516 57762 57808 57992 58430 58672 58702 59163 59247 59357 59478 59831 59844 59919 59998 60733 60836 60940 61171 61198 61357 61540 61684 61826 61931 62005 62110 62285 62582 62592 62686 62749 62963 62988 63009 63081 63102 63127 63549 63783 64043 65049 65133 65804 65939 66199 66752 66993 67003 67020 67186 67353 67392 67485 67549 67642 67763 67833 68462 68542 69042 69173 69597 69691 69743 69969 70286 70583 70620 70669 70757 70867 70969 70980 71148 71214 71347 71775 72314 72539 72649 72815 72842 73192 73555 73727 73865 73960 73969 74058 74641 74647 74956 75053 76291 76354 76361 76371 76472 76921 77061 77223 77255 77608 77801 77979 77984 78083 78321 78489 78506 78548 78581 78634 78714 78737 78776 78815 79047 79307 79381 79476 79554 79705 79811 79940 80245 80422 80437 80827 80858 80945 80951 81090 81719 81786 81900 81943 82126 82153 82349 82441 82643 82756 83316 83712 83887 84177 84192 84199 84551 84632 84681 84791 85130 85236 85474 85483 85705 86151 86437 86591 86766 86972 87291 87536 87656 87702 87839 87968 87979 88109 88906 89130 89192 89234 89290 89292 89341 89425 89784 90093 90383 90424 90568 90590 90633 90762 91226 91494 91556 92219 92418 93468 93638 93828 94226 94324 94902 95014 95188 95336 95576 96249 96254 96510 96542 96881 97609 97785 97999 98255 98645 99097 99106 99370 99411 99497 99520 99541 99844 99849 99873 99962 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. : 0.3819 s ( 0.53%) TIME: Pairwise Calc.: 0.1190 s ( 0.16%) TIME: Clustering : 0.0888 s ( 0.12%) TIME: Cluster Post. : 71.9827 s ( 99.19%) TIME: Total: 72.5724 s TIME: Analyses took 72.5725 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (78.000 MB) Box Coords, 63 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 : 1335.3115 s ( 94.83%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 72.5725 s ( 5.15%) TIME: Data File Write : 0.1671 s ( 0.01%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1408.0512 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1410.0695 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.