CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/26/15 11:14:32 | Available memory: 4381.55 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 0.0000 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]' (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: 4.1158 s TIME: Avg. throughput= 12148.4334 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 316 Coordinates out of bounds (-1) Warning: Frame 323 Coordinates out of bounds (-1) Warning: Frame 2068 Coordinates out of bounds (-1) Warning: Frame 2069 Coordinates out of bounds (-1) Warning: Frame 2763 Coordinates out of bounds (-1) Warning: Frame 8435 Coordinates out of bounds (-1) Warning: Frame 8445 Coordinates out of bounds (-1) Warning: Frame 8446 Coordinates out of bounds (-1) Warning: Frame 10982 Coordinates out of bounds (-1) Warning: Frame 11104 Coordinates out of bounds (-1) Warning: Frame 11119 Coordinates out of bounds (-1) Warning: Frame 16029 Coordinates out of bounds (-1) Warning: Frame 18924 Coordinates out of bounds (-1) Warning: Frame 18928 Coordinates out of bounds (-1) Warning: Frame 18930 Coordinates out of bounds (-1) Warning: Frame 19446 Coordinates out of bounds (-1) Warning: Frame 19448 Coordinates out of bounds (-1) Warning: Frame 19468 Coordinates out of bounds (-1) Warning: Frame 20606 Coordinates out of bounds (-1) Warning: Frame 22680 Coordinates out of bounds (-1) Warning: Frame 22683 Coordinates out of bounds (-1) Warning: Frame 22685 Coordinates out of bounds (-1) Warning: Frame 25344 Coordinates out of bounds (-1) Warning: Frame 25494 Coordinates out of bounds (-1) Warning: Frame 25508 Coordinates out of bounds (-1) Warning: Frame 25509 Coordinates out of bounds (-1) Warning: Frame 25630 Coordinates out of bounds (-1) Warning: Frame 25665 Coordinates out of bounds (-1) Warning: Frame 25666 Coordinates out of bounds (-1) Warning: Frame 28742 Coordinates out of bounds (-1) Warning: Frame 29667 Coordinates out of bounds (-1) Warning: Frame 30795 Coordinates out of bounds (-1) Warning: Frame 30799 Coordinates out of bounds (-1) Warning: Frame 30800 Coordinates out of bounds (-1) Warning: Frame 30809 Coordinates out of bounds (-1) Warning: Frame 30810 Coordinates out of bounds (-1) Warning: Frame 30813 Coordinates out of bounds (-1) Warning: Frame 30820 Coordinates out of bounds (-1) Warning: Frame 30866 Coordinates out of bounds (-1) Warning: Frame 30867 Coordinates out of bounds (-1) Warning: Frame 31821 Coordinates out of bounds (-1) Warning: Frame 33065 Coordinates out of bounds (-1) Warning: Frame 33087 Coordinates out of bounds (-1) Warning: Frame 33146 Coordinates out of bounds (-1) Warning: Frame 33147 Coordinates out of bounds (-1) Warning: Frame 33156 Coordinates out of bounds (-1) Warning: Frame 33216 Coordinates out of bounds (-1) Warning: Frame 33226 Coordinates out of bounds (-1) Warning: Frame 33227 Coordinates out of bounds (-1) Warning: Frame 33653 Coordinates out of bounds (-1) Warning: Frame 33800 Coordinates out of bounds (-1) Warning: Frame 33816 Coordinates out of bounds (-1) Warning: Frame 33817 Coordinates out of bounds (-1) Warning: Frame 33819 Coordinates out of bounds (-1) Warning: Frame 33861 Coordinates out of bounds (-1) Warning: Frame 33868 Coordinates out of bounds (-1) Warning: Frame 33899 Coordinates out of bounds (-1) Warning: Frame 33914 Coordinates out of bounds (-1) Warning: Frame 33947 Coordinates out of bounds (-1) Warning: Frame 35535 Coordinates out of bounds (-1) Warning: Frame 35536 Coordinates out of bounds (-1) Warning: Frame 35980 Coordinates out of bounds (-1) Warning: Frame 36175 Coordinates out of bounds (-1) Warning: Frame 36180 Coordinates out of bounds (-1) Warning: Frame 36889 Coordinates out of bounds (-1) Warning: Frame 36936 Coordinates out of bounds (-1) Warning: Frame 37778 Coordinates out of bounds (-1) Warning: Frame 37779 Coordinates out of bounds (-1) Warning: Frame 37784 Coordinates out of bounds (-1) Warning: Frame 37785 Coordinates out of bounds (-1) Warning: Frame 40662 Coordinates out of bounds (-1) Warning: Frame 40711 Coordinates out of bounds (-1) Warning: Frame 43457 Coordinates out of bounds (-1) Warning: Frame 43512 Coordinates out of bounds (-1) Warning: Frame 46706 Coordinates out of bounds (-1) Warning: Frame 46707 Coordinates out of bounds (-1) Warning: Frame 47748 Coordinates out of bounds (-1) Warning: Frame 49128 Coordinates out of bounds (-1) Warning: Frame 49130 Coordinates out of bounds (-1) Warning: Frame 49139 Coordinates out of bounds (-1) Warning: Frame 49587 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49919.000000 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: 4.2668 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.