CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:22:19 | Available memory: 23.491 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 8 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 8 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= 562.9387 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 8 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (168560000) Estimated pair-wise matrix memory usage: > 1.998 MB Pair-wise matrix set up with sieve, 200000 frames, 1000 sieved frames. 0% 12% 26% 30% 45% 51% 81% 83% 85% 91% 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: 992 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 64 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 64 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 50 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 17 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 2 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 24 threads 0% 11% 23% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 8 clusters 200000 frames #Cluster 0 has average-distance-to-centroid 0.714845 #Cluster 1 has average-distance-to-centroid 1.155892 #Cluster 2 has average-distance-to-centroid 0.778176 #Cluster 3 has average-distance-to-centroid 1.081635 #Cluster 4 has average-distance-to-centroid 1.084287 #Cluster 5 has average-distance-to-centroid 1.252205 #Cluster 6 has average-distance-to-centroid 1.633923 #Cluster 7 has average-distance-to-centroid 1.557615 #DBI: 1.427146 #pSF: 57930.881641 #Algorithm: Kmeans nclusters 8 maxit 100 #Representative frames: 139597 84282 93976 39798 54099 147889 164988 14044 #Sieve value: 200 (random) #Sieved frames: 13 58 163 546 582 715 765 1098 1310 1573 2000 2084 2542 3167 3200 3588 3626 3696 3840 3895 4200 4318 4418 4914 4933 4940 5677 5785 5938 6146 6211 6329 6671 7012 7109 7317 7405 7573 7668 7674 7683 8382 8606 8715 8944 9070 9185 9273 9429 9459 9563 9715 10172 10332 10404 10609 10808 11547 11643 11750 12126 12254 12291 12871 12877 12919 12962 13015 13128 13232 13249 13347 13372 13384 13611 13614 13619 13725 14044 14193 14337 14387 14406 14664 14760 14981 15509 16011 16364 16407 16559 16615 16975 17172 17247 17248 17324 17445 17712 17873 18181 18477 18639 18786 18816 18930 19191 19196 19514 19616 19767 19799 20369 20429 20448 20657 20734 20889 21294 21486 21785 22150 22258 22441 22481 22514 22973 23095 23151 23442 23584 23831 23833 23878 23938 24972 25070 25117 25202 25379 25666 26194 26271 26357 26374 26384 26440 26980 27102 27191 27222 27531 27573 27589 27740 27923 28397 28628 28682 28932 28965 29220 29405 29668 29735 29777 29963 30117 30297 30324 30568 30630 30724 30840 30963 31351 31476 31643 31674 31796 32209 32946 33025 33064 33510 33545 33675 34110 34169 34224 34360 34637 34758 34843 34903 34949 35498 35855 36056 36150 36391 37397 37531 37544 37966 37985 38150 38249 39026 39165 39486 39757 39770 39798 40103 40109 40270 40618 40758 40943 41104 41164 41440 41585 41715 42153 42306 42374 42605 43218 43262 43538 44304 44361 44636 44812 44886 45137 45200 45433 45442 45468 45969 46053 46586 46680 46886 46904 46953 47151 47519 47545 47826 48253 48288 48628 48671 48687 48776 49201 49221 49719 49759 49926 49952 50433 50503 51085 51289 51387 51400 51433 51461 51485 51605 51959 52819 52886 52977 53018 53053 53620 53670 53941 54099 54150 54283 54449 54603 54674 54692 54879 54921 55054 55180 55270 55289 55296 55356 55466 55639 55711 55931 55977 56028 56045 56390 56678 56908 57308 57315 57325 57508 57605 57690 58101 58220 58614 58722 59140 59176 59433 59477 59571 59886 60081 60641 60785 61129 61733 61787 62140 62154 62205 62215 62467 62659 62703 62783 62884 63100 63129 63220 63614 63737 63867 63951 64113 64173 64299 64726 64950 65218 65878 66047 66164 66438 66534 66561 66803 66890 66986 67021 67366 67393 67602 67635 67745 67823 67850 67873 67875 68134 68384 68840 68872 69091 69373 69923 69963 70474 70497 70664 71065 71103 71133 71264 71547 71780 71853 71854 72019 72049 72399 72537 72637 73309 73494 73501 73677 73778 73785 74301 74334 74705 74786 74925 74945 75219 75484 75505 75745 75955 76185 76199 76283 76748 76995 77432 77614 77719 77776 77837 78330 78422 78674 78900 79094 79278 79334 79388 79602 80006 80158 80191 80194 80240 80250 80287 80402 80544 80721 80952 81501 81523 81946 82194 82238 82422 82877 83403 83551 83717 83822 83862 84282 84450 85014 85739 86065 86236 86450 86578 86604 87380 87439 87574 87809 87997 88016 88188 88611 89037 89050 89080 89282 89340 89392 89635 89715 90159 91548 91582 91799 92206 92491 92711 93073 93241 93273 93495 93662 93709 93920 93976 94143 94272 94425 94555 94722 94872 95225 95681 96003 96406 96767 96917 97011 97160 97232 97340 97509 97537 97827 98165 98313 98481 98781 98787 98922 99079 99373 99442 99619 99627 99792 99991 100429 100614 100863 101035 101038 101358 101531 101600 101627 101717 101834 101870 102371 102523 102536 102683 102724 103004 103217 103439 103779 104310 104386 104892 105077 105901 105957 105961 106413 106519 106627 106843 107274 107347 107494 108193 108478 108595 108669 108675 108862 108869 108946 109313 109443 109619 109969 110150 110248 110321 110359 110492 110564 110612 110875 111314 111377 111663 111828 112059 112370 112523 112934 113341 113449 113605 113662 113733 113871 113925 114096 114232 114367 114368 114394 114449 114620 114646 115220 115374 115629 115822 116155 116183 116283 116294 116438 116685 117073 117183 117231 117251 117756 117826 118082 119113 119193 119265 119293 119820 119965 119973 120036 120177 120201 120222 120254 120476 120755 121030 121908 122125 122413 122628 122691 123173 123359 123733 124169 124180 124511 124545 124815 124825 125183 125201 125235 125259 125455 125507 125676 125699 125746 125754 125762 125778 126133 126267 126564 127061 127276 127595 127614 128162 128219 128614 128823 129037 129089 129367 129428 130173 130461 130499 130500 130543 130836 130860 131354 131762 131918 131946 132548 132647 132814 132977 133091 133659 133941 134141 134287 134485 134641 135241 135715 136222 136224 136236 136550 136659 136710 136810 137245 137298 137556 137697 137831 137974 138783 138886 138907 139065 139124 139361 139536 139597 139804 140056 140582 140701 140998 141236 141382 141550 141682 141846 142364 142468 142578 143083 143178 143269 143702 144450 144504 145019 145045 145053 145168 145732 145977 145990 146086 146201 146344 146464 147153 147352 147740 147763 147889 147951 148173 148263 148308 148545 148619 148948 149059 149340 149589 150011 150338 150389 150452 150454 150584 150598 150776 151018 151295 151713 151963 152329 152734 152778 152812 153073 153506 153636 153773 153774 153829 154183 154348 154829 154948 154996 155370 155898 156092 156208 156360 156552 156939 157029 157251 157633 157867 158001 158266 158422 158766 158796 158871 158883 158901 158917 159082 159629 159765 159897 159992 160001 160123 160494 160595 160820 160878 160958 161251 161288 161318 161524 161796 161799 162501 163024 163222 163238 163607 163942 164765 164858 164866 164988 165197 165536 165743 165823 166340 166475 167159 167539 167636 167962 168168 168220 168818 168882 168898 169108 169478 169667 169819 169901 170072 170282 170359 170441 170981 171301 171416 171620 171678 171988 172233 172360 172394 172507 172677 172719 172735 172818 172856 173627 173956 174116 175182 175748 175785 175917 176006 176083 176103 176201 176424 176486 176824 177369 177474 177642 178136 178205 178685 178725 178804 178814 179457 179706 180067 180109 180500 180866 181302 181352 181519 181661 181963 181979 182527 182629 183120 183300 183458 183804 183865 184207 184312 184909 184999 185069 185215 185293 185484 185586 185987 186044 186066 186271 186293 186343 187198 187248 187436 187485 187549 187574 187623 187828 187985 188025 188185 188335 188975 188989 189353 189390 189543 189718 189884 189964 190367 191289 192103 192421 192880 193276 193693 193819 193950 193989 194021 194029 194377 194675 194725 194768 194829 194994 195098 195201 195233 195340 195429 195871 196026 196048 196181 196867 196920 196935 197387 197431 197856 198120 198522 199182 199553 199716 199770 199999 200000 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 'ctraj.c6' as Amber NetCDF Writing 'ctraj.c7' 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. Writing 'rep.c7.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0004 s ( 0.00%) TIME: Pairwise Calc.: 1.3449 s ( 1.05%) TIME: Clustering : 0.2463 s ( 0.19%) TIME: Cluster Post. : 126.4033 s ( 98.76%) TIME: Total: 127.9949 s TIME: Analyses took 127.9950 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 : 355.2785 s ( 73.51%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 127.9950 s ( 26.48%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0082 s ( 0.00%) TIME: Run Total 483.2817 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 484.9303 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.