CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/28/15 11:22:36 | Available memory: 9894.06 MB INPUT: Reading Input from file pt-test-lowT.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 remdtraj remdtrajtemp 298.41 trajnames ../traj.1.02,../traj.1.03,../traj.1.04,../traj.1.05,../traj.1.06,../traj.1.07,../traj.1.08,../traj.1.09,../traj.1.10,../traj.1.11,../traj.1.12,../traj.1.13,../traj.1.14,../traj.1.15,../traj.1.16,../traj.1.17,../traj.1.18 ] [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 ] 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, 50000 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 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: REMD: OPENING 18 REMD TRAJECTORIES 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 ] 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. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 69.2550 s TIME: Avg. throughput= 721.9690 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 test298_hist_rmsd-all_500ns.dat norm] Hist: test298_hist_rmsd-all_500ns.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 test298_hist_rmsd-all_500ns.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 897 Coordinates out of bounds (-1) Warning: Frame 913 Coordinates out of bounds (-1) Warning: Frame 3983 Coordinates out of bounds (-1) Warning: Frame 5265 Coordinates out of bounds (-1) Warning: Frame 7413 Coordinates out of bounds (-1) Warning: Frame 7415 Coordinates out of bounds (-1) Warning: Frame 10540 Coordinates out of bounds (-1) Warning: Frame 12061 Coordinates out of bounds (-1) Warning: Frame 14879 Coordinates out of bounds (-1) Warning: Frame 15408 Coordinates out of bounds (-1) Warning: Frame 15419 Coordinates out of bounds (-1) Warning: Frame 16443 Coordinates out of bounds (-1) Warning: Frame 21329 Coordinates out of bounds (-1) Warning: Frame 22329 Coordinates out of bounds (-1) Warning: Frame 22701 Coordinates out of bounds (-1) Warning: Frame 22704 Coordinates out of bounds (-1) Warning: Frame 23172 Coordinates out of bounds (-1) Warning: Frame 25739 Coordinates out of bounds (-1) Warning: Frame 27765 Coordinates out of bounds (-1) Warning: Frame 27794 Coordinates out of bounds (-1) Warning: Frame 28092 Coordinates out of bounds (-1) Warning: Frame 32205 Coordinates out of bounds (-1) Warning: Frame 34829 Coordinates out of bounds (-1) Warning: Frame 35132 Coordinates out of bounds (-1) Warning: Frame 35134 Coordinates out of bounds (-1) Warning: Frame 35513 Coordinates out of bounds (-1) Warning: Frame 35514 Coordinates out of bounds (-1) Warning: Frame 39310 Coordinates out of bounds (-1) Warning: Frame 39311 Coordinates out of bounds (-1) Warning: Frame 41048 Coordinates out of bounds (-1) Warning: Frame 43522 Coordinates out of bounds (-1) Warning: Frame 43686 Coordinates out of bounds (-1) Warning: Frame 49365 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49967.000000 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: test298_hist_rmsd-all_500ns.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 70.8581 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.