CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/21/15 11:36:17 | Available memory: 2616.16 MB INPUT: Reading Input from file pt-sort_351.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 351.82 ] Reading 'traj.1.01' as Amber NetCDF [trajin traj.1.02 remdtrajtemp 351.82 ] Reading 'traj.1.02' as Amber NetCDF [trajin traj.1.03 remdtrajtemp 351.82 ] Reading 'traj.1.03' as Amber NetCDF [trajin traj.1.04 remdtrajtemp 351.82 ] Reading 'traj.1.04' as Amber NetCDF [trajin traj.1.05 remdtrajtemp 351.82 ] Reading 'traj.1.05' as Amber NetCDF [trajin traj.1.06 remdtrajtemp 351.82 ] Reading 'traj.1.06' as Amber NetCDF [trajin traj.1.07 remdtrajtemp 351.82 ] Reading 'traj.1.07' as Amber NetCDF [trajin traj.1.08 remdtrajtemp 351.82 ] Reading 'traj.1.08' as Amber NetCDF [trajin traj.1.09 remdtrajtemp 351.82 ] Reading 'traj.1.09' as Amber NetCDF [trajin traj.1.10 remdtrajtemp 351.82 ] Reading 'traj.1.10' as Amber NetCDF [trajin traj.1.11 remdtrajtemp 351.82 ] Reading 'traj.1.11' as Amber NetCDF [trajin traj.1.12 remdtrajtemp 351.82] Reading 'traj.1.12' as Amber NetCDF [trajin traj.2.01 remdtrajtemp 351.82] Reading 'traj.2.01' as Amber NetCDF [trajin traj.2.02 remdtrajtemp 351.82] Reading 'traj.2.02' as Amber NetCDF [trajin traj.2.03 remdtrajtemp 351.82] Reading 'traj.2.03' as Amber NetCDF [trajin traj.2.04 remdtrajtemp 351.82] Reading 'traj.2.04' as Amber NetCDF [trajin traj.2.05 remdtrajtemp 351.82] Reading 'traj.2.05' as Amber NetCDF [trajin traj.2.06 remdtrajtemp 351.82] Reading 'traj.2.06' as Amber NetCDF [trajin traj.2.07 remdtrajtemp 351.82] Reading 'traj.2.07' as Amber NetCDF [trajin traj.2.08 remdtrajtemp 351.82] Reading 'traj.2.08' as Amber NetCDF [trajin traj.2.09 remdtrajtemp 351.82] Reading 'traj.2.09' as Amber NetCDF [trajin traj.2.10 remdtrajtemp 351.82] Reading 'traj.2.10' as Amber NetCDF [trajin traj.2.11 remdtrajtemp 351.82] Reading 'traj.2.11' as Amber NetCDF [trajin traj.2.12 remdtrajtemp 351.82] 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 out rmsd-all.dat] 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 0.0040 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 out rmsd-all.dat] 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: 307.6618 s TIME: Avg. throughput= 3900.3873 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 DATAFILES: rmsd-all.dat (Standard Data File): rms_2_aform ---------- RUN END --------------------------------------------------- [hist rms_2_aform,0,5,0.1 out hist_rmsd-all_351.dat norm] Hist: hist_rmsd-all_351.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_351.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 2091 Coordinates out of bounds (-1) Warning: Frame 3542 Coordinates out of bounds (-1) Warning: Frame 3543 Coordinates out of bounds (-1) Warning: Frame 3544 Coordinates out of bounds (-1) Warning: Frame 4324 Coordinates out of bounds (-1) Warning: Frame 17049 Coordinates out of bounds (-1) Warning: Frame 17745 Coordinates out of bounds (-1) Warning: Frame 18348 Coordinates out of bounds (-1) Warning: Frame 18417 Coordinates out of bounds (-1) Warning: Frame 18429 Coordinates out of bounds (-1) Warning: Frame 18430 Coordinates out of bounds (-1) Warning: Frame 18460 Coordinates out of bounds (-1) Warning: Frame 18505 Coordinates out of bounds (-1) Warning: Frame 18633 Coordinates out of bounds (-1) Warning: Frame 18658 Coordinates out of bounds (-1) Warning: Frame 18659 Coordinates out of bounds (-1) Warning: Frame 18670 Coordinates out of bounds (-1) Warning: Frame 18671 Coordinates out of bounds (-1) Warning: Frame 18672 Coordinates out of bounds (-1) Warning: Frame 19495 Coordinates out of bounds (-1) Warning: Frame 19572 Coordinates out of bounds (-1) Warning: Frame 21281 Coordinates out of bounds (-1) Warning: Frame 23468 Coordinates out of bounds (-1) Warning: Frame 23470 Coordinates out of bounds (-1) Warning: Frame 23538 Coordinates out of bounds (-1) Warning: Frame 24590 Coordinates out of bounds (-1) Warning: Frame 24663 Coordinates out of bounds (-1) Warning: Frame 25879 Coordinates out of bounds (-1) Warning: Frame 26752 Coordinates out of bounds (-1) Warning: Frame 33141 Coordinates out of bounds (-1) Warning: Frame 33182 Coordinates out of bounds (-1) Warning: Frame 33183 Coordinates out of bounds (-1) Warning: Frame 33258 Coordinates out of bounds (-1) Warning: Frame 33259 Coordinates out of bounds (-1) Warning: Frame 34433 Coordinates out of bounds (-1) Warning: Frame 34501 Coordinates out of bounds (-1) Warning: Frame 37070 Coordinates out of bounds (-1) Warning: Frame 37121 Coordinates out of bounds (-1) Warning: Frame 37127 Coordinates out of bounds (-1) Warning: Frame 37764 Coordinates out of bounds (-1) Warning: Frame 37787 Coordinates out of bounds (-1) Warning: Frame 37792 Coordinates out of bounds (-1) Warning: Frame 37822 Coordinates out of bounds (-1) Warning: Frame 39028 Coordinates out of bounds (-1) Warning: Frame 39034 Coordinates out of bounds (-1) Warning: Frame 39040 Coordinates out of bounds (-1) Warning: Frame 39084 Coordinates out of bounds (-1) Warning: Frame 39219 Coordinates out of bounds (-1) Warning: Frame 39221 Coordinates out of bounds (-1) Warning: Frame 39224 Coordinates out of bounds (-1) Warning: Frame 39256 Coordinates out of bounds (-1) Warning: Frame 39257 Coordinates out of bounds (-1) Warning: Frame 39259 Coordinates out of bounds (-1) Warning: Frame 39260 Coordinates out of bounds (-1) Warning: Frame 39261 Coordinates out of bounds (-1) Warning: Frame 39265 Coordinates out of bounds (-1) Warning: Frame 39267 Coordinates out of bounds (-1) Warning: Frame 39273 Coordinates out of bounds (-1) Warning: Frame 40693 Coordinates out of bounds (-1) Warning: Frame 45047 Coordinates out of bounds (-1) Warning: Frame 45116 Coordinates out of bounds (-1) Warning: Frame 45124 Coordinates out of bounds (-1) Warning: Frame 45150 Coordinates out of bounds (-1) Warning: Frame 45156 Coordinates out of bounds (-1) Warning: Frame 45160 Coordinates out of bounds (-1) Warning: Frame 57502 Coordinates out of bounds (-1) Warning: Frame 57923 Coordinates out of bounds (-1) Warning: Frame 57924 Coordinates out of bounds (-1) Warning: Frame 57926 Coordinates out of bounds (-1) Warning: Frame 58629 Coordinates out of bounds (-1) Warning: Frame 58632 Coordinates out of bounds (-1) Warning: Frame 58667 Coordinates out of bounds (-1) Warning: Frame 58670 Coordinates out of bounds (-1) Warning: Frame 58671 Coordinates out of bounds (-1) Warning: Frame 58688 Coordinates out of bounds (-1) Warning: Frame 58697 Coordinates out of bounds (-1) Warning: Frame 58701 Coordinates out of bounds (-1) Warning: Frame 61183 Coordinates out of bounds (-1) Warning: Frame 62413 Coordinates out of bounds (-1) Warning: Frame 71332 Coordinates out of bounds (-1) Warning: Frame 79350 Coordinates out of bounds (-1) Warning: Frame 86283 Coordinates out of bounds (-1) Warning: Frame 86284 Coordinates out of bounds (-1) Warning: Frame 86285 Coordinates out of bounds (-1) Warning: Frame 86366 Coordinates out of bounds (-1) Warning: Frame 86385 Coordinates out of bounds (-1) Warning: Frame 86389 Coordinates out of bounds (-1) Warning: Frame 86391 Coordinates out of bounds (-1) Warning: Frame 86392 Coordinates out of bounds (-1) Warning: Frame 87645 Coordinates out of bounds (-1) Warning: Frame 90802 Coordinates out of bounds (-1) Warning: Frame 90803 Coordinates out of bounds (-1) Warning: Frame 91402 Coordinates out of bounds (-1) Warning: Frame 92185 Coordinates out of bounds (-1) Warning: Frame 95553 Coordinates out of bounds (-1) Warning: 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Frame 104550 Coordinates out of bounds (-1) Warning: Frame 104566 Coordinates out of bounds (-1) Warning: Frame 104571 Coordinates out of bounds (-1) Warning: Frame 104572 Coordinates out of bounds (-1) Warning: Frame 104621 Coordinates out of bounds (-1) Warning: Frame 104622 Coordinates out of bounds (-1) Warning: Frame 104623 Coordinates out of bounds (-1) Warning: Frame 104627 Coordinates out of bounds (-1) Warning: Frame 104630 Coordinates out of bounds (-1) Warning: Frame 113435 Coordinates out of bounds (-1) Warning: Frame 113483 Coordinates out of bounds (-1) Warning: Frame 113513 Coordinates out of bounds (-1) Warning: Frame 115231 Coordinates out of bounds (-1) Warning: Frame 115234 Coordinates out of bounds (-1) Warning: Frame 115800 Coordinates out of bounds (-1) Warning: Frame 115803 Coordinates out of bounds (-1) Warning: Frame 115804 Coordinates out of bounds (-1) Warning: Frame 118733 Coordinates out of bounds (-1) Warning: Frame 118734 Coordinates out of bounds (-1) Warning: Frame 118810 Coordinates out of bounds (-1) Warning: Frame 119443 Coordinates out of bounds (-1) Warning: Frame 119465 Coordinates out of bounds (-1) Warning: Frame 122490 Coordinates out of bounds (-1) Warning: Frame 122590 Coordinates out of bounds (-1) Warning: Frame 122592 Coordinates out of bounds (-1) Warning: Frame 122593 Coordinates out of bounds (-1) Warning: Frame 123049 Coordinates out of bounds (-1) Warning: Frame 123058 Coordinates out of bounds (-1) Warning: Frame 123059 Coordinates out of bounds (-1) Warning: Frame 123985 Coordinates out of bounds (-1) Warning: Frame 128110 Coordinates out of bounds (-1) Warning: Frame 128197 Coordinates out of bounds (-1) Warning: Frame 128483 Coordinates out of bounds (-1) Warning: Frame 130040 Coordinates out of bounds (-1) Warning: Frame 130133 Coordinates out of bounds (-1) Warning: Frame 134621 Coordinates out of bounds (-1) Warning: Frame 134623 Coordinates out of bounds (-1) Warning: Frame 135583 Coordinates out of bounds (-1) Warning: Frame 135584 Coordinates out of bounds (-1) Warning: Frame 135586 Coordinates out of bounds (-1) Warning: Frame 135608 Coordinates out of bounds (-1) Warning: Frame 136027 Coordinates out of bounds (-1) Warning: Frame 136028 Coordinates out of bounds (-1) Warning: Frame 136039 Coordinates out of bounds (-1) Warning: Frame 136045 Coordinates out of bounds (-1) Warning: Frame 137582 Coordinates out of bounds (-1) Warning: Frame 137597 Coordinates out of bounds (-1) Warning: Frame 137601 Coordinates out of bounds (-1) Warning: Frame 137602 Coordinates out of bounds (-1) Warning: Frame 137632 Coordinates out of bounds (-1) Warning: Frame 137633 Coordinates out of bounds (-1) Warning: Frame 137662 Coordinates out of bounds (-1) Warning: Frame 139779 Coordinates out of bounds (-1) Warning: Frame 139787 Coordinates out of bounds (-1) Warning: Frame 139790 Coordinates out of bounds (-1) Warning: Frame 140480 Coordinates out of bounds (-1) Warning: Frame 140492 Coordinates out of bounds (-1) Warning: Frame 140950 Coordinates out of bounds (-1) Warning: Frame 147216 Coordinates out of bounds (-1) Warning: Frame 147222 Coordinates out of bounds (-1) Warning: Frame 147223 Coordinates out of bounds (-1) Warning: Frame 147224 Coordinates out of bounds (-1) Warning: Frame 152136 Coordinates out of bounds (-1) Warning: Frame 161734 Coordinates out of bounds (-1) Warning: Frame 161753 Coordinates out of bounds (-1) Warning: Frame 164740 Coordinates out of bounds (-1) Warning: Frame 164742 Coordinates out of bounds (-1) Warning: Frame 164768 Coordinates out of bounds (-1) Warning: Frame 164794 Coordinates out of bounds (-1) Warning: Frame 167322 Coordinates out of bounds (-1) Warning: Frame 167505 Coordinates out of bounds (-1) Warning: Frame 167507 Coordinates out of bounds (-1) Warning: Frame 167525 Coordinates out of bounds (-1) Warning: Frame 167550 Coordinates out of bounds (-1) Warning: Frame 168809 Coordinates out of bounds (-1) Warning: Frame 168815 Coordinates out of bounds (-1) Warning: Frame 168824 Coordinates out of bounds (-1) Warning: Frame 168833 Coordinates out of bounds (-1) Warning: Frame 168835 Coordinates out of bounds (-1) Warning: Frame 168836 Coordinates out of bounds (-1) Warning: Frame 168837 Coordinates out of bounds (-1) Warning: Frame 168838 Coordinates out of bounds (-1) Warning: Frame 168895 Coordinates out of bounds (-1) Warning: Frame 168902 Coordinates out of bounds (-1) Warning: Frame 168909 Coordinates out of bounds (-1) Warning: Frame 168910 Coordinates out of bounds (-1) Warning: Frame 168941 Coordinates out of bounds (-1) Warning: Frame 168942 Coordinates out of bounds (-1) Warning: Frame 168946 Coordinates out of bounds (-1) Warning: Frame 168972 Coordinates out of bounds (-1) Warning: Frame 168973 Coordinates out of bounds (-1) Warning: Frame 168974 Coordinates out of bounds (-1) Warning: Frame 168982 Coordinates out of bounds (-1) Warning: Frame 175231 Coordinates out of bounds (-1) Warning: Frame 175290 Coordinates out of bounds (-1) Warning: Frame 177693 Coordinates out of bounds (-1) Warning: Frame 179020 Coordinates out of bounds (-1) Warning: Frame 189700 Coordinates out of bounds (-1) Warning: Frame 190178 Coordinates out of bounds (-1) Warning: Frame 212569 Coordinates out of bounds (-1) Warning: Frame 212603 Coordinates out of bounds (-1) Warning: Frame 212648 Coordinates out of bounds (-1) Warning: Frame 213091 Coordinates out of bounds (-1) Warning: Frame 215953 Coordinates out of bounds (-1) Warning: Frame 220991 Coordinates out of bounds (-1) Warning: Frame 221061 Coordinates out of bounds (-1) Warning: Frame 221119 Coordinates out of bounds (-1) Warning: Frame 221182 Coordinates out of bounds (-1) Warning: Frame 221185 Coordinates out of bounds (-1) Warning: Frame 221190 Coordinates out of bounds (-1) Warning: Frame 222981 Coordinates out of bounds (-1) Warning: Frame 227527 Coordinates out of bounds (-1) Warning: Frame 227530 Coordinates out of bounds (-1) Warning: Frame 227539 Coordinates out of bounds (-1) Warning: Frame 227698 Coordinates out of bounds (-1) Warning: Frame 227709 Coordinates out of bounds (-1) Warning: Frame 227714 Coordinates out of bounds (-1) Warning: Frame 228222 Coordinates out of bounds (-1) Warning: Frame 228244 Coordinates out of bounds (-1) Warning: Frame 228255 Coordinates out of bounds (-1) Warning: Frame 228260 Coordinates out of bounds (-1) Warning: Frame 228922 Coordinates out of bounds (-1) Warning: Frame 228929 Coordinates out of bounds (-1) Warning: Frame 235096 Coordinates out of bounds (-1) Warning: Frame 235101 Coordinates out of bounds (-1) Warning: Frame 235316 Coordinates out of bounds (-1) Warning: Frame 235488 Coordinates out of bounds (-1) Warning: Frame 235498 Coordinates out of bounds (-1) Warning: Frame 235499 Coordinates out of bounds (-1) Warning: Frame 236171 Coordinates out of bounds (-1) Warning: Frame 236287 Coordinates out of bounds (-1) Warning: Frame 236293 Coordinates out of bounds (-1) Warning: Frame 236302 Coordinates out of bounds (-1) Warning: Frame 236957 Coordinates out of bounds (-1) Warning: Frame 236960 Coordinates out of bounds (-1) Warning: Frame 237603 Coordinates out of bounds (-1) Warning: Frame 237604 Coordinates out of bounds (-1) Warning: Frame 237605 Coordinates out of bounds (-1) Warning: Frame 237626 Coordinates out of bounds (-1) Warning: Frame 237656 Coordinates out of bounds (-1) Warning: Frame 237994 Coordinates out of bounds (-1) Warning: Frame 237995 Coordinates out of bounds (-1) Warning: Frame 237996 Coordinates out of bounds (-1) Warning: Frame 237997 Coordinates out of bounds (-1) Warning: Frame 237999 Coordinates out of bounds (-1) Warning: Frame 238000 Coordinates out of bounds (-1) Warning: Frame 244739 Coordinates out of bounds (-1) Warning: Frame 247860 Coordinates out of bounds (-1) Warning: Frame 247868 Coordinates out of bounds (-1) Warning: Frame 247915 Coordinates out of bounds (-1) Warning: Frame 247921 Coordinates out of bounds (-1) Warning: Frame 247966 Coordinates out of bounds (-1) Warning: Frame 247984 Coordinates out of bounds (-1) Warning: Frame 247988 Coordinates out of bounds (-1) Warning: Frame 247989 Coordinates out of bounds (-1) Warning: Frame 247990 Coordinates out of bounds (-1) Warning: Frame 247991 Coordinates out of bounds (-1) Warning: Frame 247994 Coordinates out of bounds (-1) Warning: Frame 250091 Coordinates out of bounds (-1) Warning: Frame 250153 Coordinates out of bounds (-1) Warning: Frame 250163 Coordinates out of bounds (-1) Warning: Frame 252051 Coordinates out of bounds (-1) Warning: Frame 252052 Coordinates out of bounds (-1) Warning: Frame 253432 Coordinates out of bounds (-1) Warning: Frame 253433 Coordinates out of bounds (-1) Warning: Frame 253439 Coordinates out of bounds (-1) Warning: Frame 256748 Coordinates out of bounds (-1) Warning: Frame 259013 Coordinates out of bounds (-1) Warning: Frame 259015 Coordinates out of bounds (-1) Warning: Frame 262171 Coordinates out of bounds (-1) Warning: Frame 262172 Coordinates out of bounds (-1) Warning: Frame 262173 Coordinates out of bounds (-1) Warning: Frame 264889 Coordinates out of bounds (-1) Warning: Frame 264912 Coordinates out of bounds (-1) Warning: Frame 264976 Coordinates out of bounds (-1) Warning: Frame 265009 Coordinates out of bounds (-1) Warning: Frame 265010 Coordinates out of bounds (-1) Warning: Frame 265064 Coordinates out of bounds (-1) Warning: Frame 271999 Coordinates out of bounds (-1) Warning: Frame 273412 Coordinates out of bounds (-1) Warning: Frame 273434 Coordinates out of bounds (-1) Warning: Frame 273440 Coordinates out of bounds (-1) Warning: Frame 273452 Coordinates out of bounds (-1) Warning: Frame 277385 Coordinates out of bounds (-1) Warning: Frame 279259 Coordinates out of bounds (-1) Warning: Frame 279266 Coordinates out of bounds (-1) Warning: Frame 279267 Coordinates out of bounds (-1) Warning: Frame 280882 Coordinates out of bounds (-1) Warning: Frame 281787 Coordinates out of bounds (-1) Warning: Frame 281788 Coordinates out of bounds (-1) Warning: Frame 282843 Coordinates out of bounds (-1) Warning: Frame 283280 Coordinates out of bounds (-1) Warning: Frame 283283 Coordinates out of bounds (-1) Warning: Frame 283284 Coordinates out of bounds (-1) Warning: Frame 283295 Coordinates out of bounds (-1) Warning: Frame 286888 Coordinates out of bounds (-1) Warning: Frame 289894 Coordinates out of bounds (-1) Warning: Frame 289931 Coordinates out of bounds (-1) Warning: Frame 292009 Coordinates out of bounds (-1) Warning: Frame 294904 Coordinates out of bounds (-1) Warning: Frame 295085 Coordinates out of bounds (-1) Warning: Frame 295106 Coordinates out of bounds (-1) Warning: Frame 295109 Coordinates out of bounds (-1) Warning: Frame 295115 Coordinates out of bounds (-1) Warning: Frame 295117 Coordinates out of bounds (-1) Warning: Frame 295146 Coordinates out of bounds (-1) Warning: Frame 295169 Coordinates out of bounds (-1) Warning: Frame 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(-1) Warning: Frame 1153814 Coordinates out of bounds (-1) Warning: Frame 1156259 Coordinates out of bounds (-1) Warning: Frame 1156260 Coordinates out of bounds (-1) Warning: Frame 1156803 Coordinates out of bounds (-1) Warning: Frame 1156805 Coordinates out of bounds (-1) Warning: Frame 1156811 Coordinates out of bounds (-1) Warning: Frame 1156820 Coordinates out of bounds (-1) Warning: Frame 1156824 Coordinates out of bounds (-1) Warning: Frame 1156845 Coordinates out of bounds (-1) Warning: Frame 1156875 Coordinates out of bounds (-1) Warning: Frame 1158434 Coordinates out of bounds (-1) Warning: Frame 1158511 Coordinates out of bounds (-1) Warning: Frame 1160017 Coordinates out of bounds (-1) Warning: Frame 1160018 Coordinates out of bounds (-1) Warning: Frame 1160022 Coordinates out of bounds (-1) Warning: Frame 1160051 Coordinates out of bounds (-1) Warning: Frame 1160052 Coordinates out of bounds (-1) Warning: Frame 1160053 Coordinates out of bounds (-1) Warning: Frame 1160182 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(-1) Warning: Frame 1182012 Coordinates out of bounds (-1) Warning: Frame 1182061 Coordinates out of bounds (-1) Warning: Frame 1182611 Coordinates out of bounds (-1) Warning: Frame 1182614 Coordinates out of bounds (-1) Warning: Frame 1182647 Coordinates out of bounds (-1) Warning: Frame 1182738 Coordinates out of bounds (-1) Warning: Frame 1182745 Coordinates out of bounds (-1) Warning: Frame 1182750 Coordinates out of bounds (-1) Warning: Frame 1185017 Coordinates out of bounds (-1) Warning: Frame 1185055 Coordinates out of bounds (-1) Warning: Frame 1193365 Coordinates out of bounds (-1) Warning: Frame 1193366 Coordinates out of bounds (-1) Warning: Frame 1194109 Coordinates out of bounds (-1) Warning: Frame 1194117 Coordinates out of bounds (-1) Warning: Frame 1194119 Coordinates out of bounds (-1) Warning: Frame 1194774 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1198856.000000 TIME: Analyses took 0.0236 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: rmsd-all.dat (Standard Data File): rms_2_aform hist_rmsd-all_351.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 311.6880 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.