CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:35:43 | Available memory: 16.010 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 7 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 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= 25.9295 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 7 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 (148740000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 20% 30% 41% 50% 60% 70% 80% 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: 39 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 9 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 3 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 2 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 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 0.552014 #Cluster 1 has average-distance-to-centroid 0.825301 #Cluster 2 has average-distance-to-centroid 1.415278 #Cluster 3 has average-distance-to-centroid 1.306143 #Cluster 4 has average-distance-to-centroid 1.176069 #Cluster 5 has average-distance-to-centroid 1.346772 #Cluster 6 has average-distance-to-centroid 1.061595 #DBI: 1.189801 #pSF: 44784.416602 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 5806 6708 7692 87306 66383 85299 20591 #Sieve value: 200 (random) #Sieved frames: 642 717 978 1068 1168 2022 2375 2640 3177 3494 3556 3587 3987 4001 4007 4072 4288 4308 4482 4647 4933 5132 5321 5545 5585 5806 5853 5909 6324 6708 6777 7189 7334 7692 8069 8279 8824 8936 8962 8991 9140 9443 9491 10471 10720 11051 11157 11525 11672 11912 12060 12440 12729 13028 13170 13396 14100 14665 14801 15057 15113 15450 15794 15853 15971 15998 16171 16238 16395 16465 16542 16767 17105 17277 17434 18811 19107 19155 19213 19568 19657 19765 19807 19860 20078 20389 20444 20467 20490 20591 20622 20709 20761 20784 20990 21241 21577 21605 21653 21970 22325 22853 22876 23233 23294 23354 23484 23758 23800 23846 23893 24042 24234 24260 24373 24438 24478 24499 24652 24996 25065 25367 25382 25850 26122 26248 26327 26332 26395 26643 26812 26971 27224 27262 27402 27484 27689 27718 28063 28119 28196 28258 28445 28508 28565 28745 28868 28922 29281 29499 30323 30362 30598 30651 31007 31403 31720 31769 32011 32682 32688 33175 33352 33627 33738 33996 34374 34377 34698 34792 34876 35736 36110 36251 36281 36697 36966 37642 37658 37787 37887 38340 38478 38701 38843 38857 39043 39404 39584 39631 39838 39903 40126 40271 40366 40543 40607 41850 42110 42233 42474 42652 42972 43006 43211 43657 43708 43748 43755 43888 44149 44218 44301 44379 44664 45164 45296 45672 45762 46270 46356 46810 47185 47280 47309 47389 48416 48429 48686 48752 48891 48901 49034 49165 49298 49641 49729 49866 49891 50214 50509 50533 50651 50674 50761 50771 50772 50822 51276 51316 51453 51456 51683 52448 52966 53160 53405 53408 53491 53785 54054 54383 54386 54401 54458 54693 54935 54968 55087 55666 55702 55964 55971 56050 56141 56286 56292 56442 56881 57016 57110 57210 57655 57988 58637 58793 59211 59538 59736 59800 59880 60036 60057 60363 60557 60717 60886 61144 61231 61457 61476 61554 61595 61799 61949 62174 62461 63096 63172 63180 63252 63559 63762 63846 63864 63896 64102 64104 64140 64251 64574 64630 64771 64906 65021 65137 65396 65463 65731 65741 65848 66383 66399 66971 67214 67807 67840 68172 68263 68743 69263 70505 70662 70910 70941 71232 71315 71394 71460 71706 71994 72324 72353 72536 72550 72571 72691 72925 72980 73029 73683 74058 74200 74234 74719 74802 75031 75303 75449 75904 76000 76030 76147 76551 76690 76811 77029 77109 77317 77598 77961 78524 78541 78644 78759 79200 79206 79357 79465 79689 79980 80003 80079 80225 80498 80688 80797 80850 80928 81166 81239 81353 81378 81421 81448 81564 81653 82085 82319 82422 82509 82860 83043 83079 83125 83246 83248 83360 83412 83434 83442 83893 83920 84276 84411 84439 84650 85271 85299 85560 85798 85923 86603 86698 86911 87138 87299 87306 87472 87712 88019 88473 88521 88694 89243 89526 89862 90658 90733 91208 91305 91405 91538 91611 91717 91877 91879 91909 91911 91993 92010 92159 92330 92358 92430 92696 92734 93319 93373 93773 93850 94215 95213 95367 95554 95691 96003 96063 96166 96201 96692 97015 97362 97399 97402 97600 97635 97694 97732 97857 97963 98094 98213 98417 98756 98951 99129 99833 99903 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 '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. : 0.3311 s ( 0.58%) TIME: Pairwise Calc.: 0.0669 s ( 0.12%) TIME: Clustering : 0.0567 s ( 0.10%) TIME: Cluster Post. : 56.6896 s ( 99.20%) TIME: Total: 57.1443 s TIME: Analyses took 57.1444 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 : 3856.6072 s ( 98.54%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 57.1444 s ( 1.46%) TIME: Data File Write : 0.1375 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 3913.8892 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3915.2522 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.