CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/28/15 11:23:36 | Available memory: 4173.33 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: 10.2453 s TIME: Avg. throughput= 4880.2732 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 39 Coordinates out of bounds (-1) Warning: Frame 2920 Coordinates out of bounds (-1) Warning: Frame 2921 Coordinates out of bounds (-1) Warning: Frame 2931 Coordinates out of bounds (-1) Warning: Frame 2932 Coordinates out of bounds (-1) Warning: Frame 2933 Coordinates out of bounds (-1) Warning: Frame 3582 Coordinates out of bounds (-1) Warning: Frame 6461 Coordinates out of bounds (-1) Warning: Frame 6464 Coordinates out of bounds (-1) Warning: Frame 6469 Coordinates out of bounds (-1) Warning: Frame 6478 Coordinates out of bounds (-1) Warning: Frame 6892 Coordinates out of bounds (-1) Warning: Frame 6897 Coordinates out of bounds (-1) Warning: Frame 6917 Coordinates out of bounds (-1) Warning: Frame 6918 Coordinates out of bounds (-1) Warning: Frame 7485 Coordinates out of bounds (-1) Warning: Frame 7501 Coordinates out of bounds (-1) Warning: Frame 7502 Coordinates out of bounds (-1) Warning: Frame 12592 Coordinates out of bounds (-1) Warning: Frame 12609 Coordinates out of bounds (-1) Warning: Frame 12620 Coordinates out of bounds (-1) Warning: Frame 13093 Coordinates out of bounds (-1) Warning: Frame 13094 Coordinates out of bounds (-1) Warning: Frame 13101 Coordinates out of bounds (-1) Warning: Frame 13323 Coordinates out of bounds (-1) Warning: Frame 13428 Coordinates out of bounds (-1) Warning: Frame 13495 Coordinates out of bounds (-1) Warning: Frame 13962 Coordinates out of bounds (-1) Warning: Frame 14354 Coordinates out of bounds (-1) Warning: Frame 14838 Coordinates out of bounds (-1) Warning: Frame 14839 Coordinates out of bounds (-1) Warning: Frame 17087 Coordinates out of bounds (-1) Warning: Frame 17112 Coordinates out of bounds (-1) Warning: Frame 17135 Coordinates out of bounds (-1) Warning: Frame 17136 Coordinates out of bounds (-1) Warning: Frame 18546 Coordinates out of bounds (-1) Warning: Frame 18547 Coordinates out of bounds (-1) Warning: Frame 19145 Coordinates out of bounds (-1) Warning: Frame 19151 Coordinates out of bounds (-1) Warning: Frame 19152 Coordinates out of bounds (-1) Warning: Frame 19154 Coordinates out of bounds (-1) Warning: Frame 19156 Coordinates out of bounds (-1) Warning: Frame 24272 Coordinates out of bounds (-1) Warning: Frame 24276 Coordinates out of bounds (-1) Warning: Frame 24283 Coordinates out of bounds (-1) Warning: Frame 24284 Coordinates out of bounds (-1) Warning: Frame 25136 Coordinates out of bounds (-1) Warning: Frame 25137 Coordinates out of bounds (-1) Warning: Frame 25329 Coordinates out of bounds (-1) Warning: Frame 25331 Coordinates out of bounds (-1) Warning: Frame 25332 Coordinates out of bounds (-1) Warning: Frame 25707 Coordinates out of bounds (-1) Warning: Frame 25737 Coordinates out of bounds (-1) Warning: Frame 25738 Coordinates out of bounds (-1) Warning: Frame 25739 Coordinates out of bounds (-1) Warning: Frame 25741 Coordinates out of bounds (-1) Warning: Frame 25742 Coordinates out of bounds (-1) Warning: Frame 25743 Coordinates out of bounds (-1) Warning: Frame 25744 Coordinates out of bounds (-1) Warning: Frame 25745 Coordinates out of bounds (-1) Warning: Frame 25750 Coordinates out of bounds (-1) Warning: Frame 25752 Coordinates out of bounds (-1) Warning: Frame 25755 Coordinates out of bounds (-1) Warning: Frame 25760 Coordinates out of bounds (-1) Warning: Frame 25829 Coordinates out of bounds (-1) Warning: Frame 25833 Coordinates out of bounds (-1) Warning: Frame 25835 Coordinates out of bounds (-1) Warning: Frame 25845 Coordinates out of bounds (-1) Warning: Frame 25847 Coordinates out of bounds (-1) Warning: Frame 31324 Coordinates out of bounds (-1) Warning: Frame 32514 Coordinates out of bounds (-1) Warning: Frame 32526 Coordinates out of bounds (-1) Warning: Frame 34485 Coordinates out of bounds (-1) Warning: Frame 35667 Coordinates out of bounds (-1) Warning: Frame 35706 Coordinates out of bounds (-1) Warning: Frame 35707 Coordinates out of bounds (-1) Warning: Frame 35708 Coordinates out of bounds (-1) Warning: Frame 35714 Coordinates out of bounds (-1) Warning: Frame 39600 Coordinates out of bounds (-1) Warning: Frame 41704 Coordinates out of bounds (-1) Warning: Frame 42157 Coordinates out of bounds (-1) Warning: Frame 42158 Coordinates out of bounds (-1) Warning: Frame 42159 Coordinates out of bounds (-1) Warning: Frame 42174 Coordinates out of bounds (-1) Warning: Frame 42203 Coordinates out of bounds (-1) Warning: Frame 44237 Coordinates out of bounds (-1) Warning: Frame 48228 Coordinates out of bounds (-1) Warning: Frame 48251 Coordinates out of bounds (-1) Warning: Frame 48336 Coordinates out of bounds (-1) Warning: Frame 48337 Coordinates out of bounds (-1) Warning: Frame 48351 Coordinates out of bounds (-1) Warning: Frame 48621 Coordinates out of bounds (-1) Warning: Frame 48624 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49907.000000 TIME: Analyses took 0.0006 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: 10.4415 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.