CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/21/15 11:26:00 | Available memory: 1145.68 MB INPUT: Reading Input from file pt-sort.in [parm ./build/full.topo.hmr [traj]] Reading './build/full.topo.hmr' as Amber Topology [parm ../../../aa-A-form.pdb [striped]] Reading '../../../aa-A-form.pdb' as PDB File aa-A-form.pdb: determining bond info from distances. Warning: aa-A-form.pdb: Determining default bond distances from element types. [trajin traj.1.01 remdtrajtemp 298.41 ] Reading 'traj.1.01' as Amber NetCDF [trajin traj.1.02 remdtrajtemp 298.41 ] Reading 'traj.1.02' as Amber NetCDF [trajin traj.1.03 remdtrajtemp 298.41 ] Reading 'traj.1.03' as Amber NetCDF [trajin traj.1.04 remdtrajtemp 298.41 ] Reading 'traj.1.04' as Amber NetCDF [trajin traj.1.05 remdtrajtemp 298.41 ] Reading 'traj.1.05' as Amber NetCDF [trajin traj.1.06 remdtrajtemp 298.41 ] Reading 'traj.1.06' as Amber NetCDF [trajin traj.1.07 remdtrajtemp 298.41 ] Reading 'traj.1.07' as Amber NetCDF [trajin traj.1.08 remdtrajtemp 298.41 ] Reading 'traj.1.08' as Amber NetCDF [trajin traj.1.09 remdtrajtemp 298.41 ] Reading 'traj.1.09' as Amber NetCDF [trajin traj.1.10 remdtrajtemp 298.41 ] Reading 'traj.1.10' as Amber NetCDF [trajin traj.1.11 remdtrajtemp 298.41 ] Reading 'traj.1.11' as Amber NetCDF [trajin traj.1.12 remdtrajtemp 298.41 ] Reading 'traj.1.12' as Amber NetCDF [trajin traj.2.01 remdtrajtemp 298.41] Reading 'traj.2.01' as Amber NetCDF [trajin traj.2.02 remdtrajtemp 298.41] Reading 'traj.2.02' as Amber NetCDF [trajin traj.2.03 remdtrajtemp 298.41] Reading 'traj.2.03' as Amber NetCDF [trajin traj.2.04 remdtrajtemp 298.41] Reading 'traj.2.04' as Amber NetCDF [trajin traj.2.05 remdtrajtemp 298.41] Reading 'traj.2.05' as Amber NetCDF [trajin traj.2.06 remdtrajtemp 298.41] Reading 'traj.2.06' as Amber NetCDF [trajin traj.2.07 remdtrajtemp 298.41] Reading 'traj.2.07' as Amber NetCDF [trajin traj.2.08 remdtrajtemp 298.41] Reading 'traj.2.08' as Amber NetCDF [trajin traj.2.09 remdtrajtemp 298.41] Reading 'traj.2.09' as Amber NetCDF [trajin traj.2.10 remdtrajtemp 298.41] Reading 'traj.2.10' as Amber NetCDF [trajin traj.2.11 remdtrajtemp 298.41] Reading 'traj.2.11' as Amber NetCDF [trajin traj.2.12 remdtrajtemp 298.41] Reading 'traj.2.12' as Amber NetCDF [reference ../../../aa-A-form.pdb parm [striped] [a-form]] Reading '../../../aa-A-form.pdb' as PDB [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "aa-A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [run ] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 1200000 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: 'traj.1.01' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 1: 'traj.1.02' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 2: 'traj.1.03' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 3: 'traj.1.04' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 4: 'traj.1.05' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 5: 'traj.1.06' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 6: 'traj.1.07' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 7: 'traj.1.08' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 8: 'traj.1.09' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 9: 'traj.1.10' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 10: 'traj.1.11' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 11: 'traj.1.12' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 12: 'traj.2.01' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 13: 'traj.2.02' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 14: 'traj.2.03' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 15: 'traj.2.04' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 16: 'traj.2.05' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 17: 'traj.2.06' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 18: 'traj.2.07' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 19: 'traj.2.08' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 20: 'traj.2.09' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 21: 'traj.2.10' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 22: 'traj.2.11' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 23: 'traj.2.12' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) Coordinate processing will occur on 1200000 frames. REFERENCE FRAMES (1 total): 0: '../../../aa-A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: Warning: Active reference has only 65 atoms, parm '[traj]' has 3301. Warning: Parm will only have reference coordinates for the first 65 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM '[traj]' (2 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Target 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. ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.02 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.03 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.04 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.05 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.06 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.07 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.08 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.09 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.10 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.11 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.1.12 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.02 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.03 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.04 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.05 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.06 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.07 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.08 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.09 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.10 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.11 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.12 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 1200000 frames and processed 1200000 frames. TIME: Trajectory processing: 312.9797 s TIME: Avg. throughput= 3834.1150 frames / second. ACTION OUTPUT: DATASETS: 2 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 1200000 ---------- RUN END --------------------------------------------------- [hist rms_2_aform,0,5,0.1 out hist_rmsd-all_1000ns.dat norm] Hist: hist_rmsd-all_1000ns.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 1 analyses: 0: [hist rms_2_aform,0,5,0.1 out hist_rmsd-all_1000ns.dat norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 1200000 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 1523 Coordinates out of bounds (-1) Warning: Frame 1530 Coordinates out of bounds (-1) Warning: Frame 1544 Coordinates out of bounds (-1) Warning: Frame 3255 Coordinates out of bounds (-1) Warning: Frame 3256 Coordinates out of bounds (-1) Warning: Frame 6502 Coordinates out of bounds (-1) Warning: Frame 6503 Coordinates out of bounds (-1) Warning: Frame 6547 Coordinates out of bounds (-1) Warning: Frame 6559 Coordinates out of bounds (-1) Warning: Frame 6581 Coordinates out of bounds (-1) Warning: Frame 6594 Coordinates out of bounds (-1) Warning: Frame 7812 Coordinates out of bounds (-1) Warning: Frame 20017 Coordinates out of bounds (-1) Warning: Frame 20066 Coordinates out of bounds (-1) Warning: Frame 23639 Coordinates out of bounds (-1) Warning: Frame 25250 Coordinates out of bounds (-1) Warning: Frame 25277 Coordinates out of bounds (-1) Warning: Frame 31431 Coordinates out of bounds (-1) Warning: Frame 31437 Coordinates out of bounds (-1) Warning: Frame 31447 Coordinates out of bounds (-1) Warning: Frame 31459 Coordinates out of bounds (-1) Warning: Frame 31466 Coordinates out of bounds (-1) Warning: Frame 31505 Coordinates out of bounds (-1) Warning: Frame 31525 Coordinates out of bounds (-1) Warning: Frame 31529 Coordinates out of bounds (-1) Warning: Frame 31537 Coordinates out of bounds (-1) Warning: Frame 35024 Coordinates out of bounds (-1) Warning: Frame 41979 Coordinates out of bounds (-1) Warning: Frame 41980 Coordinates out of bounds (-1) Warning: Frame 42008 Coordinates out of bounds (-1) Warning: Frame 42039 Coordinates out of bounds (-1) Warning: Frame 48086 Coordinates out of bounds (-1) Warning: Frame 48164 Coordinates out of bounds (-1) Warning: Frame 48167 Coordinates out of bounds (-1) Warning: Frame 48172 Coordinates out of bounds (-1) Warning: Frame 48174 Coordinates out of bounds (-1) Warning: Frame 48178 Coordinates out of bounds (-1) Warning: Frame 48179 Coordinates out of bounds (-1) Warning: Frame 48226 Coordinates out of bounds (-1) Warning: Frame 56293 Coordinates out of bounds (-1) Warning: Frame 56295 Coordinates out of bounds (-1) Warning: Frame 56296 Coordinates out of bounds (-1) Warning: Frame 56298 Coordinates out of bounds (-1) Warning: Frame 56301 Coordinates out of bounds (-1) Warning: Frame 56338 Coordinates out of bounds (-1) Warning: Frame 56340 Coordinates out of bounds (-1) Warning: Frame 56878 Coordinates out of bounds (-1) Warning: Frame 56947 Coordinates out of bounds (-1) Warning: Frame 56957 Coordinates out of bounds (-1) Warning: Frame 56967 Coordinates out of bounds (-1) Warning: Frame 56975 Coordinates out of bounds (-1) Warning: Frame 57136 Coordinates out of bounds (-1) Warning: Frame 67735 Coordinates out of bounds (-1) Warning: Frame 67736 Coordinates out of bounds (-1) Warning: Frame 67738 Coordinates out of bounds (-1) Warning: Frame 70223 Coordinates out of bounds (-1) Warning: Frame 73374 Coordinates out of bounds (-1) Warning: Frame 73375 Coordinates out of bounds (-1) Warning: Frame 78507 Coordinates out of bounds (-1) Warning: Frame 78509 Coordinates out of bounds (-1) Warning: Frame 78510 Coordinates out of bounds (-1) Warning: Frame 78511 Coordinates out of bounds (-1) Warning: Frame 78616 Coordinates out of bounds (-1) Warning: Frame 78617 Coordinates out of bounds (-1) Warning: Frame 78621 Coordinates out of bounds (-1) Warning: Frame 78624 Coordinates out of bounds (-1) Warning: Frame 78626 Coordinates out of bounds (-1) Warning: Frame 78628 Coordinates out of bounds (-1) Warning: Frame 78629 Coordinates out of bounds (-1) Warning: Frame 81958 Coordinates out of bounds (-1) Warning: Frame 84296 Coordinates out of bounds (-1) Warning: Frame 84347 Coordinates out of bounds (-1) Warning: Frame 84349 Coordinates out of bounds (-1) Warning: Frame 84350 Coordinates out of bounds (-1) Warning: Frame 84356 Coordinates out of bounds (-1) Warning: Frame 84361 Coordinates out of bounds (-1) Warning: 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121385 Coordinates out of bounds (-1) Warning: Frame 128494 Coordinates out of bounds (-1) Warning: Frame 128511 Coordinates out of bounds (-1) Warning: Frame 128512 Coordinates out of bounds (-1) Warning: Frame 129354 Coordinates out of bounds (-1) Warning: Frame 132535 Coordinates out of bounds (-1) Warning: Frame 158067 Coordinates out of bounds (-1) Warning: Frame 160976 Coordinates out of bounds (-1) Warning: Frame 165341 Coordinates out of bounds (-1) Warning: Frame 165348 Coordinates out of bounds (-1) Warning: Frame 165350 Coordinates out of bounds (-1) Warning: Frame 165353 Coordinates out of bounds (-1) Warning: Frame 165373 Coordinates out of bounds (-1) Warning: Frame 165435 Coordinates out of bounds (-1) Warning: Frame 165436 Coordinates out of bounds (-1) Warning: Frame 165739 Coordinates out of bounds (-1) Warning: Frame 165740 Coordinates out of bounds (-1) Warning: Frame 165766 Coordinates out of bounds (-1) Warning: Frame 165779 Coordinates out of bounds (-1) Warning: 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Warning: Frame 174303 Coordinates out of bounds (-1) Warning: Frame 174304 Coordinates out of bounds (-1) Warning: Frame 183860 Coordinates out of bounds (-1) Warning: Frame 183868 Coordinates out of bounds (-1) Warning: Frame 190182 Coordinates out of bounds (-1) Warning: Frame 190683 Coordinates out of bounds (-1) Warning: Frame 190738 Coordinates out of bounds (-1) Warning: Frame 194079 Coordinates out of bounds (-1) Warning: Frame 198749 Coordinates out of bounds (-1) Warning: Frame 200210 Coordinates out of bounds (-1) Warning: Frame 200221 Coordinates out of bounds (-1) Warning: Frame 200226 Coordinates out of bounds (-1) Warning: Frame 200237 Coordinates out of bounds (-1) Warning: Frame 200238 Coordinates out of bounds (-1) Warning: Frame 204040 Coordinates out of bounds (-1) Warning: Frame 205390 Coordinates out of bounds (-1) Warning: Frame 205399 Coordinates out of bounds (-1) Warning: Frame 205400 Coordinates out of bounds (-1) Warning: Frame 205412 Coordinates out of bounds (-1) Warning: Frame 205515 Coordinates out of bounds (-1) Warning: Frame 206241 Coordinates out of bounds (-1) Warning: Frame 210038 Coordinates out of bounds (-1) Warning: Frame 210039 Coordinates out of bounds (-1) Warning: Frame 210079 Coordinates out of bounds (-1) Warning: Frame 224768 Coordinates out of bounds (-1) Warning: Frame 224772 Coordinates out of bounds (-1) Warning: Frame 225976 Coordinates out of bounds (-1) Warning: Frame 226014 Coordinates out of bounds (-1) Warning: Frame 226015 Coordinates out of bounds (-1) Warning: Frame 226016 Coordinates out of bounds (-1) Warning: Frame 228219 Coordinates out of bounds (-1) Warning: Frame 228299 Coordinates out of bounds (-1) Warning: Frame 228411 Coordinates out of bounds (-1) Warning: Frame 228912 Coordinates out of bounds (-1) Warning: Frame 230494 Coordinates out of bounds (-1) Warning: Frame 230495 Coordinates out of bounds (-1) Warning: Frame 230519 Coordinates out of bounds (-1) Warning: Frame 230528 Coordinates out of bounds (-1) Warning: Frame 230533 Coordinates out of bounds (-1) Warning: Frame 230535 Coordinates out of bounds (-1) Warning: Frame 230854 Coordinates out of bounds (-1) Warning: Frame 230947 Coordinates out of bounds (-1) Warning: Frame 231981 Coordinates out of bounds (-1) Warning: Frame 231982 Coordinates out of bounds (-1) Warning: Frame 231984 Coordinates out of bounds (-1) Warning: Frame 232707 Coordinates out of bounds (-1) Warning: Frame 236732 Coordinates out of bounds (-1) Warning: Frame 236739 Coordinates out of bounds (-1) Warning: Frame 236775 Coordinates out of bounds (-1) Warning: Frame 236831 Coordinates out of bounds (-1) Warning: Frame 238193 Coordinates out of bounds (-1) Warning: Frame 239759 Coordinates out of bounds (-1) Warning: Frame 239879 Coordinates out of bounds (-1) Warning: Frame 242707 Coordinates out of bounds (-1) Warning: Frame 242708 Coordinates out of bounds (-1) Warning: Frame 245290 Coordinates out of bounds (-1) Warning: Frame 245292 Coordinates out of bounds (-1) Warning: Frame 245296 Coordinates out of bounds (-1) Warning: Frame 245306 Coordinates out of bounds (-1) Warning: Frame 245317 Coordinates out of bounds (-1) Warning: Frame 245319 Coordinates out of bounds (-1) Warning: Frame 245327 Coordinates out of bounds (-1) Warning: Frame 245335 Coordinates out of bounds (-1) Warning: Frame 245339 Coordinates out of bounds (-1) Warning: Frame 245353 Coordinates out of bounds (-1) Warning: Frame 245364 Coordinates out of bounds (-1) Warning: Frame 245368 Coordinates out of bounds (-1) Warning: Frame 245471 Coordinates out of bounds (-1) Warning: Frame 245613 Coordinates out of bounds (-1) Warning: Frame 245616 Coordinates out of bounds (-1) Warning: Frame 245621 Coordinates out of bounds (-1) Warning: Frame 245624 Coordinates out of bounds (-1) Warning: Frame 245641 Coordinates out of bounds (-1) Warning: Frame 250049 Coordinates out of bounds (-1) Warning: Frame 254281 Coordinates out of bounds (-1) Warning: Frame 258399 Coordinates out of bounds (-1) Warning: Frame 261358 Coordinates out of bounds (-1) Warning: Frame 261359 Coordinates out of bounds (-1) Warning: Frame 263835 Coordinates out of bounds (-1) Warning: Frame 263907 Coordinates out of bounds (-1) Warning: Frame 263909 Coordinates out of bounds (-1) Warning: Frame 263934 Coordinates out of bounds (-1) Warning: Frame 263962 Coordinates out of bounds (-1) Warning: Frame 282168 Coordinates out of bounds (-1) Warning: Frame 282170 Coordinates out of bounds (-1) Warning: Frame 282172 Coordinates out of bounds (-1) Warning: Frame 283639 Coordinates out of bounds (-1) Warning: Frame 283655 Coordinates out of bounds (-1) Warning: Frame 283710 Coordinates out of bounds (-1) Warning: Frame 283713 Coordinates out of bounds (-1) Warning: Frame 283752 Coordinates out of bounds (-1) Warning: Frame 283803 Coordinates out of bounds (-1) Warning: Frame 283809 Coordinates out of bounds (-1) Warning: Frame 283822 Coordinates out of bounds (-1) Warning: Frame 283844 Coordinates out of bounds (-1) Warning: Frame 283852 Coordinates out of bounds (-1) Warning: Frame 283853 Coordinates out of bounds (-1) Warning: Frame 290171 Coordinates out of bounds (-1) Warning: Frame 290356 Coordinates out of bounds (-1) Warning: Frame 290360 Coordinates out of bounds (-1) Warning: Frame 292473 Coordinates out of bounds (-1) Warning: Frame 292485 Coordinates out of bounds (-1) Warning: Frame 292504 Coordinates out of bounds (-1) Warning: Frame 292603 Coordinates out of bounds (-1) Warning: Frame 292605 Coordinates out of bounds (-1) Warning: Frame 292610 Coordinates out of bounds (-1) Warning: Frame 292611 Coordinates out of bounds (-1) Warning: Frame 292612 Coordinates out of bounds (-1) Warning: Frame 292619 Coordinates out of bounds (-1) Warning: Frame 292629 Coordinates out of bounds (-1) Warning: Frame 292694 Coordinates out of bounds (-1) Warning: Frame 292697 Coordinates out of bounds (-1) Warning: Frame 293228 Coordinates out of bounds (-1) Warning: Frame 293229 Coordinates out of bounds (-1) Warning: Frame 293251 Coordinates out of bounds (-1) Warning: Frame 295972 Coordinates out of bounds (-1) Warning: Frame 295980 Coordinates out of bounds (-1) Warning: Frame 295981 Coordinates out of bounds (-1) Warning: Frame 296275 Coordinates out of bounds (-1) Warning: Frame 296292 Coordinates out of bounds (-1) Warning: Frame 297964 Coordinates out of bounds (-1) Warning: Frame 297966 Coordinates out of bounds (-1) Warning: Frame 297971 Coordinates out of bounds (-1) Warning: Frame 297972 Coordinates out of bounds (-1) Warning: Frame 297973 Coordinates out of bounds (-1) Warning: Frame 297976 Coordinates out of bounds (-1) Warning: Frame 297977 Coordinates out of bounds (-1) Warning: Frame 299258 Coordinates out of bounds (-1) Warning: Frame 306472 Coordinates out of bounds (-1) Warning: Frame 306473 Coordinates out of bounds (-1) Warning: Frame 306554 Coordinates out of bounds (-1) Warning: Frame 306556 Coordinates out of bounds (-1) Warning: Frame 306557 Coordinates out of bounds (-1) Warning: Frame 307243 Coordinates out of bounds (-1) Warning: Frame 307244 Coordinates out of bounds (-1) Warning: Frame 307267 Coordinates out of bounds (-1) Warning: Frame 307918 Coordinates out of bounds (-1) Warning: Frame 307920 Coordinates out of bounds (-1) Warning: Frame 307932 Coordinates out of bounds (-1) Warning: Frame 307957 Coordinates out of bounds (-1) Warning: Frame 307960 Coordinates out of bounds (-1) Warning: Frame 312441 Coordinates out of bounds (-1) Warning: Frame 315792 Coordinates out of bounds (-1) Warning: Frame 315806 Coordinates out of bounds (-1) Warning: Frame 316461 Coordinates out of bounds (-1) Warning: Frame 317307 Coordinates out of bounds (-1) Warning: Frame 317308 Coordinates out of bounds (-1) Warning: Frame 317311 Coordinates out of bounds (-1) Warning: Frame 317322 Coordinates out of bounds (-1) Warning: Frame 317410 Coordinates out of bounds (-1) Warning: Frame 317430 Coordinates out of bounds (-1) Warning: Frame 317435 Coordinates out of bounds (-1) Warning: Frame 317443 Coordinates out of bounds (-1) Warning: Frame 317453 Coordinates out of bounds (-1) Warning: Frame 317455 Coordinates out of bounds (-1) Warning: Frame 317456 Coordinates out of bounds (-1) Warning: Frame 317459 Coordinates out of bounds (-1) Warning: Frame 317475 Coordinates out of bounds (-1) Warning: Frame 317478 Coordinates out of bounds (-1) Warning: Frame 317485 Coordinates out of bounds (-1) Warning: Frame 317495 Coordinates out of bounds (-1) Warning: Frame 317496 Coordinates out of bounds (-1) Warning: Frame 317499 Coordinates out of bounds (-1) Warning: Frame 318147 Coordinates out of bounds (-1) Warning: Frame 318241 Coordinates out of bounds (-1) Warning: Frame 318251 Coordinates out of bounds (-1) Warning: Frame 318368 Coordinates out of bounds (-1) Warning: Frame 318372 Coordinates out of bounds (-1) Warning: Frame 321130 Coordinates out of bounds (-1) Warning: Frame 321369 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(-1) Warning: Frame 1139916 Coordinates out of bounds (-1) Warning: Frame 1140190 Coordinates out of bounds (-1) Warning: Frame 1140191 Coordinates out of bounds (-1) Warning: Frame 1140194 Coordinates out of bounds (-1) Warning: Frame 1140344 Coordinates out of bounds (-1) Warning: Frame 1140365 Coordinates out of bounds (-1) Warning: Frame 1140807 Coordinates out of bounds (-1) Warning: Frame 1140809 Coordinates out of bounds (-1) Warning: Frame 1140810 Coordinates out of bounds (-1) Warning: Frame 1140818 Coordinates out of bounds (-1) Warning: Frame 1145434 Coordinates out of bounds (-1) Warning: Frame 1145439 Coordinates out of bounds (-1) Warning: Frame 1145444 Coordinates out of bounds (-1) Warning: Frame 1145614 Coordinates out of bounds (-1) Warning: Frame 1147335 Coordinates out of bounds (-1) Warning: Frame 1147336 Coordinates out of bounds (-1) Warning: Frame 1151447 Coordinates out of bounds (-1) Warning: Frame 1153088 Coordinates out of bounds (-1) Warning: Frame 1153126 Coordinates out of bounds (-1) Warning: Frame 1157595 Coordinates out of bounds (-1) Warning: Frame 1157597 Coordinates out of bounds (-1) Warning: Frame 1159722 Coordinates out of bounds (-1) Warning: Frame 1166728 Coordinates out of bounds (-1) Warning: Frame 1170856 Coordinates out of bounds (-1) Warning: Frame 1170873 Coordinates out of bounds (-1) Warning: Frame 1170888 Coordinates out of bounds (-1) Warning: Frame 1170889 Coordinates out of bounds (-1) Warning: Frame 1170891 Coordinates out of bounds (-1) Warning: Frame 1170892 Coordinates out of bounds (-1) Warning: Frame 1174937 Coordinates out of bounds (-1) Warning: Frame 1175933 Coordinates out of bounds (-1) Warning: Frame 1175934 Coordinates out of bounds (-1) Warning: Frame 1175947 Coordinates out of bounds (-1) Warning: Frame 1186281 Coordinates out of bounds (-1) Warning: Frame 1186413 Coordinates out of bounds (-1) Warning: Frame 1186416 Coordinates out of bounds (-1) Warning: Frame 1197894 Coordinates out of bounds (-1) Warning: Frame 1197909 Coordinates out of bounds (-1) Warning: Frame 1197911 Coordinates out of bounds (-1) Warning: Frame 1197966 Coordinates out of bounds (-1) Warning: Frame 1199571 Coordinates out of bounds (-1) Warning: Frame 1199645 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1198849.000000 TIME: Analyses took 0.0156 seconds. DATASETS: 3 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 1200000 Hist_00002 "Hist_00002" (double), size is 50 DATAFILES: hist_rmsd-all_1000ns.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 315.5249 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.