CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:21:02 | Available memory: 15.111 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 rms_1_2 :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 data rms_1_2 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 dataset rms_1_2 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 rms_1_2 :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= 81.6334 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster data rms_1_2 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. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (191700000) 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: 10 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 8 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 14 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 14 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 5 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: 1 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 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 0.098301 #Cluster 1 has average-distance-to-centroid 0.143852 #Cluster 2 has average-distance-to-centroid 0.162382 #Cluster 3 has average-distance-to-centroid 0.154509 #Cluster 4 has average-distance-to-centroid 0.225481 #DBI: 0.535980 #pSF: 298076.636436 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 16388 88977 52196 43712 64800 #Sieve value: 200 (random) #Sieved frames: 53 326 904 1129 1244 1422 2104 2567 3008 3097 3111 3140 3820 4084 4277 4357 4541 5040 5130 5335 5338 5350 5460 5696 5848 5851 6173 6352 6665 7202 7326 7711 8307 8372 8443 8497 8595 8834 8915 9175 9449 9489 9864 9950 10247 10319 10492 10519 10760 10771 10973 11077 11135 11207 11500 11975 12036 12401 12677 12823 13340 13502 13594 14517 14707 15009 15100 15188 15345 15593 15598 15808 15835 15910 16015 16181 16388 16479 16485 16543 16954 17017 17227 17346 17953 18572 18690 18696 18996 19062 19240 19441 19485 19565 19626 19753 19824 20010 20357 20862 20866 20896 20905 21021 22480 22500 22590 22748 22843 22883 23144 23161 23443 23449 24212 24467 24607 25073 25093 25214 25751 25966 25992 26177 26648 26675 26784 26872 27062 27275 27485 27604 27934 28084 28140 28609 28639 28794 28911 28935 28971 29163 29174 29259 29265 29762 29768 29774 29862 30630 30730 30782 30846 30856 30890 30999 31465 31717 31787 32261 32305 32318 32436 32618 32757 32761 32795 32865 33452 33923 34938 35019 35105 35241 35504 35596 35906 35938 36048 36091 36249 36299 36352 36683 36812 36869 37106 37110 38170 38325 38616 38670 38831 38874 39275 39301 39760 39917 39922 40003 40062 40063 40069 40601 40719 40738 40842 40869 41577 41894 41938 41999 42406 42581 42648 42652 42710 42763 43121 43288 43290 43501 43525 43712 43811 43861 43985 44241 44519 44548 44758 44858 45012 45193 45619 46088 46269 46402 47202 47344 47394 47620 48009 48651 48944 49209 49545 49706 49986 50029 50084 50572 50626 50948 51461 51685 52196 52474 52523 52562 52575 52699 53022 53038 53051 53389 53607 53650 53685 54031 54141 54664 54728 54778 54826 54840 55244 55561 55963 56216 56233 56899 56983 57811 57881 57882 58078 58258 59090 59238 59497 59706 60039 60294 60347 60377 60555 60720 60909 60939 61325 61440 61533 63301 63365 63600 63960 63975 64332 64359 64393 64597 64775 64798 64800 64885 65285 65638 65726 65778 66187 66347 66423 66617 66777 66898 67003 67084 67316 67489 67526 67609 67717 67883 68137 68354 68789 68825 68846 68932 69034 69048 69115 69489 69608 69710 69766 69851 70035 70065 70093 70294 70331 70536 70544 70621 70640 70671 71012 71755 71854 71989 72147 72156 72214 72396 72448 72537 72570 72975 73296 73460 73560 73802 73871 74003 74004 74029 74129 74204 74498 74635 74636 75377 75464 75538 75591 76001 76143 76194 76289 76667 76840 76866 77305 77597 77661 77721 77726 77830 77902 77944 78172 78197 78644 78761 78780 78808 79404 79414 79468 79700 80171 80420 80725 80742 80748 81300 81396 81493 81500 81728 81806 82654 83268 83269 83342 83989 84018 84174 84207 84382 84606 84630 84766 84895 85061 85129 85430 85445 85558 85595 86745 87001 87013 87218 87469 87855 87984 88323 88977 89001 89199 89271 89393 89923 89980 90346 90843 90988 91502 91555 91567 92184 92203 92677 92714 92741 92840 93040 93164 93190 93319 93320 93607 93736 94127 94281 95204 95268 95624 96789 97564 97843 97929 98151 98261 98745 98866 99031 99208 99318 99348 99552 99574 99586 99591 99714 99856 99941 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. : 0.2843 s ( 0.39%) TIME: Pairwise Calc.: 0.0618 s ( 0.09%) TIME: Clustering : 0.0050 s ( 0.01%) TIME: Cluster Post. : 72.3334 s ( 99.52%) TIME: Total: 72.6845 s TIME: Analyses took 72.6846 seconds. DATASETS (3 total): rms_1_2 "rms_1_2" (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 : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1224.9886 s ( 94.40%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 72.6846 s ( 5.60%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0004 s ( 0.00%) TIME: Run Total 1297.6736 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1302.8419 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.