CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/23/15 11:12:38 | Available memory: 10973.5 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 [trajin ../traj.2.18] Reading '../traj.2.18' as Amber NetCDF [trajin ../traj.2.18] Reading '../traj.2.18' 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, 84928 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) 1: 'traj.2.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 17464 of 17464) 2: 'traj.2.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 17464 of 17464) Coordinate processing will occur on 84928 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 0.0047 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. ----- traj.2.18 (1-17464, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.18 (1-17464, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 84928 frames and processed 84928 frames. TIME: Trajectory processing: 7.5399 s TIME: Avg. throughput= 11263.7650 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 84928 ---------- 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: 84928 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 650 Coordinates out of bounds (-1) Warning: Frame 652 Coordinates out of bounds (-1) Warning: Frame 671 Coordinates out of bounds (-1) Warning: Frame 2572 Coordinates out of bounds (-1) Warning: Frame 3156 Coordinates out of bounds (-1) Warning: Frame 3158 Coordinates out of bounds (-1) Warning: Frame 3181 Coordinates out of bounds (-1) Warning: Frame 3182 Coordinates out of bounds (-1) Warning: Frame 4810 Coordinates out of bounds (-1) Warning: Frame 4815 Coordinates out of bounds (-1) Warning: Frame 4816 Coordinates out of bounds (-1) Warning: Frame 4817 Coordinates out of bounds (-1) Warning: Frame 5403 Coordinates out of bounds (-1) Warning: Frame 5416 Coordinates out of bounds (-1) Warning: Frame 5426 Coordinates out of bounds (-1) Warning: Frame 5808 Coordinates out of bounds (-1) Warning: Frame 5811 Coordinates out of bounds (-1) Warning: Frame 5888 Coordinates out of bounds (-1) Warning: Frame 5895 Coordinates out of bounds (-1) Warning: Frame 5914 Coordinates out of bounds (-1) Warning: Frame 5917 Coordinates out of bounds (-1) Warning: Frame 5919 Coordinates out of bounds (-1) Warning: Frame 11773 Coordinates out of bounds (-1) Warning: Frame 11774 Coordinates out of bounds (-1) Warning: Frame 11776 Coordinates out of bounds (-1) Warning: Frame 11779 Coordinates out of bounds (-1) Warning: Frame 11782 Coordinates out of bounds (-1) Warning: Frame 11788 Coordinates out of bounds (-1) Warning: Frame 11959 Coordinates out of bounds (-1) Warning: Frame 12429 Coordinates out of bounds (-1) Warning: Frame 12435 Coordinates out of bounds (-1) Warning: Frame 12442 Coordinates out of bounds (-1) Warning: Frame 12497 Coordinates out of bounds (-1) Warning: Frame 12498 Coordinates out of bounds (-1) Warning: Frame 12511 Coordinates out of bounds (-1) Warning: Frame 12618 Coordinates out of bounds (-1) Warning: Frame 13833 Coordinates out of bounds (-1) Warning: Frame 13869 Coordinates out of bounds (-1) Warning: Frame 13870 Coordinates out of bounds (-1) Warning: Frame 13871 Coordinates out of bounds (-1) Warning: Frame 13892 Coordinates out of bounds (-1) Warning: Frame 13894 Coordinates out of bounds (-1) Warning: Frame 13903 Coordinates out of bounds (-1) Warning: Frame 16050 Coordinates out of bounds (-1) Warning: Frame 16064 Coordinates out of bounds (-1) Warning: Frame 16068 Coordinates out of bounds (-1) Warning: Frame 16110 Coordinates out of bounds (-1) Warning: Frame 16192 Coordinates out of bounds (-1) Warning: Frame 16194 Coordinates out of bounds (-1) Warning: Frame 17217 Coordinates out of bounds (-1) Warning: Frame 17221 Coordinates out of bounds (-1) Warning: Frame 17239 Coordinates out of bounds (-1) Warning: Frame 17240 Coordinates out of bounds (-1) Warning: Frame 17557 Coordinates out of bounds (-1) Warning: Frame 17559 Coordinates out of bounds (-1) Warning: Frame 20305 Coordinates out of bounds (-1) Warning: Frame 22141 Coordinates out of bounds (-1) Warning: Frame 22143 Coordinates out of bounds (-1) Warning: Frame 22144 Coordinates out of bounds (-1) Warning: Frame 22254 Coordinates out of bounds (-1) Warning: Frame 22263 Coordinates out of bounds (-1) Warning: Frame 22310 Coordinates out of bounds (-1) Warning: Frame 22314 Coordinates out of bounds (-1) Warning: Frame 22653 Coordinates out of bounds (-1) Warning: Frame 24341 Coordinates out of bounds (-1) Warning: Frame 24347 Coordinates out of bounds (-1) Warning: Frame 24348 Coordinates out of bounds (-1) Warning: Frame 24355 Coordinates out of bounds (-1) Warning: Frame 24356 Coordinates out of bounds (-1) Warning: Frame 26333 Coordinates out of bounds (-1) Warning: Frame 26345 Coordinates out of bounds (-1) Warning: Frame 26347 Coordinates out of bounds (-1) Warning: Frame 26355 Coordinates out of bounds (-1) Warning: Frame 26378 Coordinates out of bounds (-1) Warning: Frame 26424 Coordinates out of bounds (-1) Warning: Frame 27015 Coordinates out of bounds (-1) Warning: Frame 27908 Coordinates out of bounds (-1) Warning: Frame 28305 Coordinates out of bounds (-1) Warning: Frame 28325 Coordinates out of bounds (-1) Warning: Frame 29588 Coordinates out of bounds (-1) Warning: Frame 29665 Coordinates out of bounds (-1) Warning: Frame 29667 Coordinates out of bounds (-1) Warning: Frame 29682 Coordinates out of bounds (-1) Warning: Frame 29693 Coordinates out of bounds (-1) Warning: Frame 29718 Coordinates out of bounds (-1) Warning: Frame 29728 Coordinates out of bounds (-1) Warning: Frame 29736 Coordinates out of bounds (-1) Warning: Frame 29739 Coordinates out of bounds (-1) Warning: Frame 29741 Coordinates out of bounds (-1) Warning: Frame 29743 Coordinates out of bounds (-1) Warning: Frame 29747 Coordinates out of bounds (-1) Warning: Frame 29748 Coordinates out of bounds (-1) Warning: Frame 29754 Coordinates out of bounds (-1) Warning: Frame 29763 Coordinates out of bounds (-1) Warning: Frame 34051 Coordinates out of bounds (-1) Warning: Frame 34052 Coordinates out of bounds (-1) Warning: Frame 34096 Coordinates out of bounds (-1) Warning: Frame 34098 Coordinates out of bounds (-1) Warning: Frame 34104 Coordinates out of bounds (-1) Warning: Frame 41001 Coordinates out of bounds (-1) Warning: Frame 41002 Coordinates out of bounds (-1) Warning: Frame 41728 Coordinates out of bounds (-1) Warning: Frame 41769 Coordinates out of bounds (-1) Warning: Frame 41772 Coordinates out of bounds (-1) Warning: Frame 41774 Coordinates out of bounds (-1) Warning: Frame 41776 Coordinates out of bounds (-1) Warning: Frame 41910 Coordinates out of bounds (-1) Warning: Frame 41912 Coordinates out of bounds (-1) Warning: Frame 41918 Coordinates out of bounds (-1) Warning: Frame 41919 Coordinates out of bounds (-1) Warning: Frame 41955 Coordinates out of bounds (-1) Warning: Frame 42435 Coordinates out of bounds (-1) Warning: Frame 42436 Coordinates out of bounds (-1) Warning: Frame 42437 Coordinates out of bounds (-1) Warning: Frame 42442 Coordinates out of bounds (-1) Warning: Frame 42474 Coordinates out of bounds (-1) Warning: Frame 45368 Coordinates out of bounds (-1) Warning: Frame 45370 Coordinates out of bounds (-1) Warning: Frame 45422 Coordinates out of bounds (-1) Warning: Frame 45424 Coordinates out of bounds (-1) Warning: Frame 46016 Coordinates out of bounds (-1) Warning: Frame 46023 Coordinates out of bounds (-1) Warning: Frame 46024 Coordinates out of bounds (-1) Warning: Frame 46054 Coordinates out of bounds (-1) Warning: Frame 46103 Coordinates out of bounds (-1) Warning: Frame 46169 Coordinates out of bounds (-1) Warning: Frame 49277 Coordinates out of bounds (-1) Warning: Frame 49947 Coordinates out of bounds (-1) Warning: Frame 52749 Coordinates out of bounds (-1) Warning: Frame 52753 Coordinates out of bounds (-1) Warning: Frame 52756 Coordinates out of bounds (-1) Warning: Frame 53536 Coordinates out of bounds (-1) Warning: Frame 53545 Coordinates out of bounds (-1) Warning: Frame 53547 Coordinates out of bounds (-1) Warning: Frame 53549 Coordinates out of bounds (-1) Warning: Frame 54809 Coordinates out of bounds (-1) Warning: Frame 54810 Coordinates out of bounds (-1) Warning: Frame 54879 Coordinates out of bounds (-1) Warning: Frame 54880 Coordinates out of bounds (-1) Warning: Frame 56910 Coordinates out of bounds (-1) Warning: Frame 56924 Coordinates out of bounds (-1) Warning: Frame 56935 Coordinates out of bounds (-1) Warning: Frame 56936 Coordinates out of bounds (-1) Warning: Frame 58146 Coordinates out of bounds (-1) Warning: Frame 58154 Coordinates out of bounds (-1) Warning: Frame 58155 Coordinates out of bounds (-1) Warning: Frame 58180 Coordinates out of bounds (-1) Warning: Frame 58181 Coordinates out of bounds (-1) Warning: Frame 58182 Coordinates out of bounds (-1) Warning: Frame 58183 Coordinates out of bounds (-1) Warning: Frame 58187 Coordinates out of bounds (-1) Warning: Frame 59267 Coordinates out of bounds (-1) Warning: Frame 62072 Coordinates out of bounds (-1) Warning: Frame 62073 Coordinates out of bounds (-1) Warning: Frame 63675 Coordinates out of bounds (-1) Warning: Frame 65123 Coordinates out of bounds (-1) Warning: Frame 65132 Coordinates out of bounds (-1) Warning: Frame 65146 Coordinates out of bounds (-1) Warning: Frame 65178 Coordinates out of bounds (-1) Warning: Frame 65181 Coordinates out of bounds (-1) Warning: Frame 65202 Coordinates out of bounds (-1) Warning: Frame 65696 Coordinates out of bounds (-1) Warning: Frame 65727 Coordinates out of bounds (-1) Warning: Frame 65731 Coordinates out of bounds (-1) Warning: Frame 65735 Coordinates out of bounds (-1) Warning: Frame 66252 Coordinates out of bounds (-1) Warning: Frame 66260 Coordinates out of bounds (-1) Warning: Frame 67109 Coordinates out of bounds (-1) Warning: Frame 67120 Coordinates out of bounds (-1) Warning: Frame 67121 Coordinates out of bounds (-1) Warning: Frame 70213 Coordinates out of bounds (-1) Warning: Frame 70217 Coordinates out of bounds (-1) Warning: Frame 70220 Coordinates out of bounds (-1) Warning: Frame 71000 Coordinates out of bounds (-1) Warning: Frame 71009 Coordinates out of bounds (-1) Warning: Frame 71011 Coordinates out of bounds (-1) Warning: Frame 71013 Coordinates out of bounds (-1) Warning: Frame 72273 Coordinates out of bounds (-1) Warning: Frame 72274 Coordinates out of bounds (-1) Warning: Frame 72343 Coordinates out of bounds (-1) Warning: Frame 72344 Coordinates out of bounds (-1) Warning: Frame 74374 Coordinates out of bounds (-1) Warning: Frame 74388 Coordinates out of bounds (-1) Warning: Frame 74399 Coordinates out of bounds (-1) Warning: Frame 74400 Coordinates out of bounds (-1) Warning: Frame 75610 Coordinates out of bounds (-1) Warning: Frame 75618 Coordinates out of bounds (-1) Warning: Frame 75619 Coordinates out of bounds (-1) Warning: Frame 75644 Coordinates out of bounds (-1) Warning: Frame 75645 Coordinates out of bounds (-1) Warning: Frame 75646 Coordinates out of bounds (-1) Warning: Frame 75647 Coordinates out of bounds (-1) Warning: Frame 75651 Coordinates out of bounds (-1) Warning: Frame 76731 Coordinates out of bounds (-1) Warning: Frame 79536 Coordinates out of bounds (-1) Warning: Frame 79537 Coordinates out of bounds (-1) Warning: Frame 81139 Coordinates out of bounds (-1) Warning: Frame 82587 Coordinates out of bounds (-1) Warning: Frame 82596 Coordinates out of bounds (-1) Warning: Frame 82610 Coordinates out of bounds (-1) Warning: Frame 82642 Coordinates out of bounds (-1) Warning: Frame 82645 Coordinates out of bounds (-1) Warning: Frame 82666 Coordinates out of bounds (-1) Warning: Frame 83160 Coordinates out of bounds (-1) Warning: Frame 83191 Coordinates out of bounds (-1) Warning: Frame 83195 Coordinates out of bounds (-1) Warning: Frame 83199 Coordinates out of bounds (-1) Warning: Frame 83716 Coordinates out of bounds (-1) Warning: Frame 83724 Coordinates out of bounds (-1) Warning: Frame 84573 Coordinates out of bounds (-1) Warning: Frame 84584 Coordinates out of bounds (-1) Warning: Frame 84585 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 84716.000000 TIME: Analyses took 0.0050 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 84928 Hist_00002 "Hist_00002" (double), size is 50 DATAFILES: hist_rmsd_18.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 9.5609 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.