CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 17:30:40 | Available memory: 65.304 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 :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, 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= 47.2258 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 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (141280000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 10% 21% 30% 40% 51% 60% 72% 82% 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: 495 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 50 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 30 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 22 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 44 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 56 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 29 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 11 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 2 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 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 0.843872 #Cluster 1 has average-distance-to-centroid 0.743363 #Cluster 2 has average-distance-to-centroid 1.486241 #Cluster 3 has average-distance-to-centroid 1.277494 #Cluster 4 has average-distance-to-centroid 1.435904 #DBI: 1.155975 #pSF: 46537.739924 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 2280 75748 42467 70218 68218 #Sieve value: 200 (random) #Sieved frames: 174 624 762 831 844 1140 1190 1440 1536 1604 2113 2250 2280 2341 2485 2512 2596 2604 2622 2658 2742 2785 3389 3405 3506 3812 4004 4410 4689 4834 5079 5266 5283 5337 5578 5900 5944 6495 6510 6678 6903 7005 7025 7049 7208 7270 7403 7572 7591 7618 7771 8006 8289 8358 8739 8744 9180 9460 9645 10072 10174 10308 10345 10355 10579 10998 11129 11140 11144 11274 11293 12008 12022 12396 12768 13019 13171 13914 14111 14329 14402 14597 14655 14717 14781 14963 15031 15187 15219 15227 15230 15407 15733 15846 16224 16258 16368 17055 17084 17121 17171 17196 17262 17689 17714 17869 18164 18770 18816 18905 19000 19037 19378 19635 19697 19834 19849 20043 20517 21462 21606 21828 22318 22434 22473 22636 22904 23145 23340 23357 23532 23553 23774 23888 24109 24346 24617 24772 25216 25746 26062 26094 26207 26247 26333 26572 26675 26973 27065 27078 27151 27855 28220 28411 28524 28703 28704 29838 30223 30249 30268 30486 30615 31021 31122 31128 31198 31305 31559 31612 31640 31717 32014 32210 32352 32829 33026 33225 33370 33431 33705 34111 34494 34545 34963 35612 35692 35796 35827 35860 35998 36188 37744 37806 38295 38388 38580 39102 39244 39305 39612 39697 39719 39953 40454 40509 41456 41494 42467 42731 42860 43229 43469 43685 43933 44624 44866 45066 45105 45289 45299 45484 45601 45612 45985 46150 46398 46636 46995 47727 47857 47898 47948 48141 48316 48389 48460 48508 48588 48894 49310 49392 49517 49571 49738 50158 50245 50256 50634 50791 50905 51065 51169 51203 51240 51309 51468 51650 51784 51907 51977 52047 52376 52808 52812 52926 53032 53473 53796 53948 54088 54585 54670 54821 54881 55325 55442 55463 55720 55845 55896 57248 57617 57637 58380 58458 58570 58769 59309 59368 59385 59848 59860 59872 60094 60216 60300 60393 60530 60762 60845 61074 61161 61254 61329 61591 61600 61993 62032 62089 62307 62814 62932 62993 63046 63359 63418 63759 64172 64223 64562 65097 65172 65301 65437 65665 66085 66390 67307 67329 67517 67547 67714 68218 68246 68379 68402 68654 68900 68923 69531 70075 70218 70351 70413 70550 70712 70997 71443 71791 71806 71995 72257 72750 73165 73246 73339 73362 73642 73653 73946 73972 74164 74290 74310 74718 74999 75293 75465 75494 75562 75613 75681 75748 76003 76133 76147 76197 76602 76639 76864 77354 77472 77487 77499 77974 77989 78059 78300 78411 78455 78570 79027 79096 79341 79418 79890 79938 79983 80260 80384 80399 81277 81482 81542 81587 81671 81816 81907 82528 82571 82783 82943 82996 83031 83062 83215 83532 84102 84191 84457 84528 85217 85258 85364 85615 85859 85881 86468 87094 87767 87851 88041 88054 88194 88223 88499 88760 89245 89339 89561 89563 89595 89943 90136 90386 90473 90612 90721 90722 90980 91012 91671 91716 92129 92398 92550 92894 93077 93166 93281 93481 93529 93658 93716 94036 94037 94239 94281 94588 94636 95592 95699 95894 96112 96156 96382 96434 96587 96595 96666 96729 97116 97187 97379 97436 97665 97778 97971 98150 98228 98532 98662 98749 98765 98918 99049 99679 99726 99738 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. : 0.0220 s ( 0.02%) TIME: Pairwise Calc.: 0.1460 s ( 0.16%) TIME: Clustering : 0.0655 s ( 0.07%) TIME: Cluster Post. : 90.2352 s ( 99.74%) TIME: Total: 90.4687 s TIME: Analyses took 90.4930 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 : 0.0000 s ( 0.00%) TIME: Trajectory Process : 2117.4881 s ( 95.90%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 90.4930 s ( 4.10%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2207.9813 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2232.0253 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.