CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:20:27 | Available memory: 9.332 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 ../../../aa/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run1/traj.1.02,../../../aa/tip3p/ff12sb/run1/traj.1.03,../../../aa/tip3p/ff12sb/run1/traj.1.04,../../../aa/tip3p/ff12sb/run1/traj.1.05,../../../aa/tip3p/ff12sb/run1/traj.1.06,../../../aa/tip3p/ff12sb/run1/traj.1.07,../../../aa/tip3p/ff12sb/run1/traj.1.08,../../../aa/tip3p/ff12sb/run1/traj.1.09,../../../aa/tip3p/ff12sb/run1/traj.1.10,../../../aa/tip3p/ff12sb/run1/traj.1.11,../../../aa/tip3p/ff12sb/run1/traj.1.12,../../../aa/tip3p/ff12sb/run1/traj.1.13,../../../aa/tip3p/ff12sb/run1/traj.1.14,../../../aa/tip3p/ff12sb/run1/traj.1.15,../../../aa/tip3p/ff12sb/run1/traj.1.16,../../../aa/tip3p/ff12sb/run1/traj.1.17,../../../aa/tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run2/traj.1.02,../../../aa/tip3p/ff12sb/run2/traj.1.03,../../../aa/tip3p/ff12sb/run2/traj.1.04,../../../aa/tip3p/ff12sb/run2/traj.1.05,../../../aa/tip3p/ff12sb/run2/traj.1.06,../../../aa/tip3p/ff12sb/run2/traj.1.07,../../../aa/tip3p/ff12sb/run2/traj.1.08,../../../aa/tip3p/ff12sb/run2/traj.1.09,../../../aa/tip3p/ff12sb/run2/traj.1.10,../../../aa/tip3p/ff12sb/run2/traj.1.11,../../../aa/tip3p/ff12sb/run2/traj.1.12,../../../aa/tip3p/ff12sb/run2/traj.1.13,../../../aa/tip3p/ff12sb/run2/traj.1.14,../../../aa/tip3p/ff12sb/run2/traj.1.15,../../../aa/tip3p/ff12sb/run2/traj.1.16,../../../aa/tip3p/ff12sb/run2/traj.1.17,../../../aa/tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [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. [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 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000] 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 150000 200000 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, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (4 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 2: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 3: 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 200000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (3 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Reference mask: [:1-2&!@H*](41) 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. 2: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (200000 frames): 7.927 GB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% ----- traj.1.01 (1-50000, 1) ----- 30% 40% ----- traj.1.01 (1-50000, 1) ----- 50% 60% 70% ----- traj.1.01 (1-50000, 1) ----- 80% 90% 100% Complete. Read 200000 frames and processed 200000 frames. TIME: Avg. throughput= 676.3945 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 50000,100000,150000,200000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Loading pair-wise distances from CpptrajPairDist Loading pair-wise distances failed - regenerating from frames. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (167820000) Estimated pair-wise matrix memory usage: > 1.998 MB Pair-wise matrix set up with sieve, 200000 frames, 1000 sieved frames. 0% 10% 20% 31% 41% 51% 60% 70% 80% 90% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 2.998 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 994 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 146 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 139 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 44 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 21 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 10 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 13 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 14 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 15 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 5 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 2 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 24 threads 0% 11% 23% 30% 44% 60% 60% 73% 80% 95% Complete. #Clustering: 6 clusters 200000 frames #Cluster 0 has average-distance-to-centroid 0.786326 #Cluster 1 has average-distance-to-centroid 1.201478 #Cluster 2 has average-distance-to-centroid 1.148932 #Cluster 3 has average-distance-to-centroid 1.194308 #Cluster 4 has average-distance-to-centroid 1.364391 #Cluster 5 has average-distance-to-centroid 1.766023 #DBI: 1.430362 #pSF: 59481.678822 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 49089 108257 48033 17015 153016 188576 #Sieve value: 200 (random) #Sieved frames: 261 861 1074 1097 1209 1467 1521 1523 1647 1773 2026 2101 2150 2202 2307 2340 2570 2656 2746 3040 3084 3456 3641 3652 3726 3925 4004 4938 5054 5146 5419 5454 5511 5786 6302 6825 7161 7230 7287 7449 7867 8268 8411 8555 8822 8968 9126 9134 9292 9395 9530 9573 10010 10127 10534 10555 10583 10648 10677 10694 11067 11385 11393 11460 11794 11955 12070 12075 12207 12500 12505 12542 12555 12750 13409 13767 13789 13817 13823 13968 13995 14139 14453 14488 14580 14654 15113 15447 15862 16453 16514 17015 17368 18791 18887 19272 19287 19289 19522 19571 19671 19702 19905 20037 20201 20222 20318 20597 20937 21029 21082 21339 21346 21360 21482 21634 21651 21844 22806 23281 23316 23428 23825 24094 24567 24723 25704 25761 25851 26344 26461 26572 26616 26702 26751 26814 27167 27297 27336 27497 27562 27642 27823 28038 28261 28464 28788 28834 29053 29192 29600 29779 29899 30489 30524 30625 30836 30962 30981 30987 31066 31155 31370 31429 31612 31688 31839 31995 32053 32183 32328 32641 32803 32922 33218 33598 33867 33882 33981 33988 34330 34475 34877 34900 35061 36489 36684 36880 37512 37649 37653 37709 37831 38260 39101 39213 39441 39877 39952 39996 40010 40299 40405 40455 40518 40727 40740 41135 41361 41449 41738 42026 42051 43031 43142 43186 43238 43437 43443 43740 44119 44146 44781 45271 45985 46140 46291 46582 46646 47570 47719 47848 47920 47970 48033 48064 48234 48242 48419 49057 49089 49119 49452 49544 49703 49806 49985 50907 50920 51258 51366 51416 52329 52387 52452 52569 52678 53201 53223 53243 53287 53364 53442 53450 53797 53885 53954 54310 54366 54434 54510 54830 54844 54850 54874 55009 55534 55570 55975 56176 56262 57177 57211 57532 57692 57827 57982 58179 58366 58908 58943 59188 59444 59748 59974 60041 60232 60476 60479 60524 60591 60933 61061 61708 61796 61844 62044 62113 62169 62780 63130 63390 63399 63544 63683 63955 64325 64409 64550 64655 65180 65291 65437 65735 65905 65967 66043 66402 66502 66784 66805 66876 66879 66942 67059 67182 67520 67585 68053 68086 68483 68554 68570 68795 69480 70025 70031 70276 70305 70310 70360 70386 70446 70756 70806 70931 71031 71056 71128 71613 71758 71884 71960 71976 72038 72227 72360 72621 72624 73059 73105 73109 73181 73515 73647 73908 73950 74008 74121 75205 75726 75745 75817 75976 76364 76464 76657 76701 76712 76833 77071 77154 77732 77834 78035 78060 78140 78235 78336 78453 78455 78600 78666 79022 79062 79080 79087 79288 79685 79807 80235 80377 80456 80623 81260 81432 81584 81923 82361 82473 82499 82665 82794 83526 83911 84568 84885 85292 85436 85511 86028 86462 86727 86794 87252 87799 87805 87807 88142 88199 88295 88516 88816 88905 88972 89325 89720 89765 90027 90281 90501 90578 90631 90974 91150 91216 91342 91575 91844 91958 91989 92014 92094 92107 92170 92217 92524 92749 92766 92859 92886 92901 93185 93455 93567 93646 93682 93771 93938 94013 94218 94652 94977 95009 95236 95335 95356 95360 95438 95547 95664 95882 96102 96306 96309 96351 96922 97310 97514 97515 97586 97723 97761 97796 98003 98125 98699 99067 99877 100045 100282 100517 101002 101192 102070 102432 102586 102919 103006 103097 103113 103142 103217 103414 103415 103999 104155 104220 104256 104546 104685 104943 105130 105173 105216 105252 105316 105789 105801 106505 106871 107224 107347 107360 107598 107671 107754 107804 107873 108257 108572 108579 108655 108918 109097 109351 109414 109449 109717 109895 110478 110747 110754 110817 111105 111613 111965 112325 112674 112690 112784 113084 113210 113251 113262 113301 113501 113729 113921 114125 114325 114359 114411 114681 114764 114848 114872 114883 115197 115412 115505 115584 115808 116651 116812 116870 117059 117337 117407 117498 117742 117774 118411 118547 119143 119209 119433 119635 119641 119836 120315 120320 120438 120549 120854 120984 121441 121513 121786 122593 122728 122802 122955 122972 123224 123646 123814 123839 124038 124089 124108 124731 124790 125014 125183 125384 125505 125904 126125 126255 126300 126478 126664 126699 127041 127826 127892 127963 127985 128210 128457 129033 129255 129621 129959 130392 130468 130783 130801 131050 131457 131505 131843 131925 131971 132183 132391 132500 132709 132953 133022 133039 133172 133191 133596 133682 133989 134164 134165 134238 134580 134747 134760 134834 134892 134949 134963 135027 135126 135135 135239 135271 135319 135430 135605 135665 136041 136291 136305 136517 136640 136829 137194 137323 137346 137365 137419 137806 138015 138922 139061 139319 139614 140163 140387 140710 140817 141044 141077 141138 141381 141884 141938 142162 142573 143030 143044 143241 143448 143519 143952 144144 144566 144908 145283 145341 145636 146333 146682 146685 147124 147206 147276 147635 147701 148011 148425 148955 148971 149173 149280 149353 149363 149414 149582 149699 150054 150222 150265 150658 150898 150961 151930 152332 152832 152898 153016 153132 153182 153258 153268 153988 154165 154411 154436 154531 154542 154775 155499 155676 155796 156014 156293 156304 156371 156394 156489 156573 157127 157147 157923 157936 158119 158381 158555 158588 158932 159023 159046 159296 159360 159632 159739 159762 159961 160500 160648 161091 161567 162135 162283 162404 162820 163061 163677 163681 163843 163933 164065 164151 164227 164331 164512 164714 164788 165319 165377 165451 165731 166032 166037 166258 166546 166882 167059 167101 167167 167652 167900 168207 168210 168339 168532 168647 168857 168861 168883 168923 169100 169131 169691 169825 170048 170056 170380 170452 170502 170805 170821 170944 171159 171358 171676 172426 172585 172592 172607 172650 172679 172783 172852 173103 173126 173610 173699 173757 173869 173922 173931 174020 174031 174080 174303 174758 174845 174887 174969 175217 175418 175584 175588 176500 176508 176700 177267 177318 177449 177528 178061 178480 178583 178689 178777 178992 179056 179069 179508 179548 180297 180332 180470 180563 180637 180640 181007 181282 181309 181363 181375 181796 182049 182105 182159 182852 183682 183896 184252 185183 185472 185535 185570 185714 185804 185860 186011 186526 186623 186676 186818 186856 186949 187120 187398 187464 187739 187985 188206 188525 188576 188652 188790 189016 189734 189931 190341 190510 190729 190832 190853 191556 191819 191832 192298 192375 192479 192571 192647 192837 192890 192940 193049 193090 193473 193522 193723 193895 194094 194356 195033 195042 195225 195230 195477 195844 195846 195909 196002 196189 196344 196959 197351 197591 198305 198487 198598 198960 199488 199764 199831 199998 Warning: split frame 200000 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. : 0.0005 s ( 0.00%) TIME: Pairwise Calc.: 1.7206 s ( 1.25%) TIME: Clustering : 0.2706 s ( 0.20%) TIME: Cluster Post. : 135.2758 s ( 98.55%) TIME: Total: 137.2675 s TIME: Analyses took 137.2679 seconds. DATASETS (4 total): [tip3p-ff12sb] "[tip3p-ff12sb]" (topology), size is 3301 full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent RMSD_00001 "RMSD_00001" (double, rms), size is 200000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 200000 (7.927 GB) Box Coords, 3301 atoms Cnum_00003 "Cnum_00003" (integer), size is 200000 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 295.6854 s ( 68.29%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 137.2679 s ( 31.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0085 s ( 0.00%) TIME: Run Total 432.9619 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 433.5872 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.