CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/28/15 11:25:10 | Available memory: 2428.59 MB INPUT: Reading Input from file pt-rmsd.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.1.18 ] Reading '../traj.1.18' as Amber NetCDF [reference ../../../../aa-A-form.pdb parm [striped] [a-form]] Reading '../../../../aa-A-form.pdb' as PDB [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd rms_2_aform :1,2&!@H= ref [a-form]] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "aa-A-form.pdb" (:1,2&!@H*), with fitting. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: 'traj.1.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) Coordinate processing will occur on 50000 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]' (3 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd rms_2_aform :1,2&!@H= ref [a-form]] 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.1.18 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 5.6366 s TIME: Avg. throughput= 8870.6162 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 50000 ---------- RUN END --------------------------------------------------- [hist rms_2_aform,0,5,0.1 out hist_rmsd_18.dat norm] Hist: hist_rmsd_18.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_18.dat norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 1145 Coordinates out of bounds (-1) Warning: Frame 1156 Coordinates out of bounds (-1) Warning: Frame 4273 Coordinates out of bounds (-1) Warning: Frame 4277 Coordinates out of bounds (-1) Warning: Frame 4279 Coordinates out of bounds (-1) Warning: Frame 6563 Coordinates out of bounds (-1) Warning: Frame 6573 Coordinates out of bounds (-1) Warning: Frame 6575 Coordinates out of bounds (-1) Warning: Frame 6582 Coordinates out of bounds (-1) Warning: Frame 8816 Coordinates out of bounds (-1) Warning: Frame 8852 Coordinates out of bounds (-1) Warning: Frame 8858 Coordinates out of bounds (-1) Warning: Frame 8859 Coordinates out of bounds (-1) Warning: Frame 8863 Coordinates out of bounds (-1) Warning: Frame 9454 Coordinates out of bounds (-1) Warning: Frame 9479 Coordinates out of bounds (-1) Warning: Frame 9496 Coordinates out of bounds (-1) Warning: Frame 9498 Coordinates out of bounds (-1) Warning: Frame 9517 Coordinates out of bounds (-1) Warning: Frame 9549 Coordinates out of bounds (-1) Warning: Frame 11413 Coordinates out of bounds (-1) Warning: Frame 11415 Coordinates out of bounds (-1) Warning: Frame 11419 Coordinates out of bounds (-1) Warning: Frame 11430 Coordinates out of bounds (-1) Warning: Frame 14072 Coordinates out of bounds (-1) Warning: Frame 14074 Coordinates out of bounds (-1) Warning: Frame 14080 Coordinates out of bounds (-1) Warning: Frame 14105 Coordinates out of bounds (-1) Warning: Frame 14106 Coordinates out of bounds (-1) Warning: Frame 16538 Coordinates out of bounds (-1) Warning: Frame 16541 Coordinates out of bounds (-1) Warning: Frame 19299 Coordinates out of bounds (-1) Warning: Frame 19313 Coordinates out of bounds (-1) Warning: Frame 19321 Coordinates out of bounds (-1) Warning: Frame 19601 Coordinates out of bounds (-1) Warning: Frame 20883 Coordinates out of bounds (-1) Warning: Frame 20901 Coordinates out of bounds (-1) Warning: Frame 20902 Coordinates out of bounds (-1) Warning: Frame 20907 Coordinates out of bounds (-1) Warning: Frame 20917 Coordinates out of bounds (-1) Warning: Frame 20932 Coordinates out of bounds (-1) Warning: Frame 20933 Coordinates out of bounds (-1) Warning: Frame 20937 Coordinates out of bounds (-1) Warning: Frame 22324 Coordinates out of bounds (-1) Warning: Frame 22341 Coordinates out of bounds (-1) Warning: Frame 22348 Coordinates out of bounds (-1) Warning: Frame 22349 Coordinates out of bounds (-1) Warning: Frame 22363 Coordinates out of bounds (-1) Warning: Frame 24317 Coordinates out of bounds (-1) Warning: Frame 25082 Coordinates out of bounds (-1) Warning: Frame 25207 Coordinates out of bounds (-1) Warning: Frame 25987 Coordinates out of bounds (-1) Warning: Frame 27204 Coordinates out of bounds (-1) Warning: Frame 27205 Coordinates out of bounds (-1) Warning: Frame 27206 Coordinates out of bounds (-1) Warning: Frame 27207 Coordinates out of bounds (-1) Warning: Frame 32025 Coordinates out of bounds (-1) Warning: Frame 32673 Coordinates out of bounds (-1) Warning: Frame 32674 Coordinates out of bounds (-1) Warning: Frame 32709 Coordinates out of bounds (-1) Warning: Frame 33273 Coordinates out of bounds (-1) Warning: Frame 33632 Coordinates out of bounds (-1) Warning: Frame 33634 Coordinates out of bounds (-1) Warning: Frame 33640 Coordinates out of bounds (-1) Warning: Frame 33641 Coordinates out of bounds (-1) Warning: Frame 33659 Coordinates out of bounds (-1) Warning: Frame 33693 Coordinates out of bounds (-1) Warning: Frame 34326 Coordinates out of bounds (-1) Warning: Frame 34328 Coordinates out of bounds (-1) Warning: Frame 34664 Coordinates out of bounds (-1) Warning: Frame 36043 Coordinates out of bounds (-1) Warning: Frame 36047 Coordinates out of bounds (-1) Warning: Frame 37422 Coordinates out of bounds (-1) Warning: Frame 37436 Coordinates out of bounds (-1) Warning: Frame 37443 Coordinates out of bounds (-1) Warning: Frame 38427 Coordinates out of bounds (-1) Warning: Frame 40126 Coordinates out of bounds (-1) Warning: Frame 40127 Coordinates out of bounds (-1) Warning: Frame 41195 Coordinates out of bounds (-1) Warning: Frame 43460 Coordinates out of bounds (-1) Warning: Frame 43554 Coordinates out of bounds (-1) Warning: Frame 43603 Coordinates out of bounds (-1) Warning: Frame 43613 Coordinates out of bounds (-1) Warning: Frame 43614 Coordinates out of bounds (-1) Warning: Frame 44710 Coordinates out of bounds (-1) Warning: Frame 47166 Coordinates out of bounds (-1) Warning: Frame 47167 Coordinates out of bounds (-1) Warning: Frame 48132 Coordinates out of bounds (-1) Warning: Frame 48995 Coordinates out of bounds (-1) Warning: Frame 48998 Coordinates out of bounds (-1) Warning: Frame 48999 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49909.000000 TIME: Analyses took 0.0005 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 50000 Hist_00002 "Hist_00002" (double), size is 50 DATAFILES: hist_rmsd_18.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7.1138 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.