CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/20/15 16:16:36 | Available memory: 10342.6 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 [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, 600000 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) Coordinate processing will occur on 600000 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 0.0000 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. Read 600000 frames and processed 600000 frames. TIME: Trajectory processing: 139.0489 s TIME: Avg. throughput= 4315.0283 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 600000 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: 600000 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 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Warning: Frame 393486 Coordinates out of bounds (-1) Warning: Frame 396466 Coordinates out of bounds (-1) Warning: Frame 398873 Coordinates out of bounds (-1) Warning: Frame 398874 Coordinates out of bounds (-1) Warning: Frame 400372 Coordinates out of bounds (-1) Warning: Frame 400504 Coordinates out of bounds (-1) Warning: Frame 404206 Coordinates out of bounds (-1) Warning: Frame 404207 Coordinates out of bounds (-1) Warning: Frame 404213 Coordinates out of bounds (-1) Warning: Frame 404214 Coordinates out of bounds (-1) Warning: Frame 406814 Coordinates out of bounds (-1) Warning: Frame 406835 Coordinates out of bounds (-1) Warning: Frame 406836 Coordinates out of bounds (-1) Warning: Frame 406837 Coordinates out of bounds (-1) Warning: Frame 409196 Coordinates out of bounds (-1) Warning: Frame 409199 Coordinates out of bounds (-1) Warning: Frame 409200 Coordinates out of bounds (-1) Warning: Frame 409207 Coordinates out of bounds (-1) Warning: Frame 415181 Coordinates out of 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Warning: Frame 557975 Coordinates out of bounds (-1) Warning: Frame 559405 Coordinates out of bounds (-1) Warning: Frame 559410 Coordinates out of bounds (-1) Warning: Frame 559458 Coordinates out of bounds (-1) Warning: Frame 559459 Coordinates out of bounds (-1) Warning: Frame 559460 Coordinates out of bounds (-1) Warning: Frame 559461 Coordinates out of bounds (-1) Warning: Frame 559544 Coordinates out of bounds (-1) Warning: Frame 559546 Coordinates out of bounds (-1) Warning: Frame 559554 Coordinates out of bounds (-1) Warning: Frame 559555 Coordinates out of bounds (-1) Warning: Frame 559556 Coordinates out of bounds (-1) Warning: Frame 560007 Coordinates out of bounds (-1) Warning: Frame 560008 Coordinates out of bounds (-1) Warning: Frame 561705 Coordinates out of bounds (-1) Warning: Frame 561707 Coordinates out of bounds (-1) Warning: Frame 561708 Coordinates out of bounds (-1) Warning: Frame 561709 Coordinates out of bounds (-1) Warning: Frame 561712 Coordinates out of bounds (-1) Warning: Frame 561744 Coordinates out of bounds (-1) Warning: Frame 561747 Coordinates out of bounds (-1) Warning: Frame 561763 Coordinates out of bounds (-1) Warning: Frame 567063 Coordinates out of bounds (-1) Warning: Frame 567064 Coordinates out of bounds (-1) Warning: Frame 569749 Coordinates out of bounds (-1) Warning: Frame 576462 Coordinates out of bounds (-1) Warning: Frame 580857 Coordinates out of bounds (-1) Warning: Frame 580907 Coordinates out of bounds (-1) Warning: Frame 587765 Coordinates out of bounds (-1) Warning: Frame 587787 Coordinates out of bounds (-1) Warning: Frame 587888 Coordinates out of bounds (-1) Warning: Frame 587889 Coordinates out of bounds (-1) Warning: Frame 587890 Coordinates out of bounds (-1) Warning: Frame 598650 Coordinates out of bounds (-1) Warning: Frame 598687 Coordinates out of bounds (-1) Warning: Frame 599418 Coordinates out of bounds (-1) Warning: Frame 599420 Coordinates out of bounds (-1) Warning: Frame 599486 Coordinates out of bounds (-1) Warning: Frame 599487 Coordinates out of bounds (-1) Warning: Frame 599499 Coordinates out of bounds (-1) Warning: Frame 599552 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 599487.000000 TIME: Analyses took 0.0041 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 600000 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: 140.6065 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.