CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/29/15 10:15:01 | Available memory: 2554.32 MB INPUT: Reading Input from file pt-ensemble.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. [ensemble ../traj.1.01 start 1 stop 100 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] [ensemble ../traj.2.01 tart 1 stop 100 rajnames ../traj.2.02,../traj.2.03,../traj.2.04,../traj.2.05,../traj.2.06,../traj.2.07,../traj.2.08,../traj.2.09,../traj.2.10,../traj.2.11,../traj.2.12,../traj.2.13,../traj.2.14,../traj.2.15,../traj.2.16,../traj.2.17,../traj.2.18] Found 18 replicas. Warning: RemdTraj: Replica ../traj.2.08 frames (17330) does not match Warning: # frames in first replica (17331). Warning: RemdTraj: Setting total # of frames to 17330 Warning: RemdTraj: Replica ../traj.2.09 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.10 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.11 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.12 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.13 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.14 frames (17331) does not match Warning: # frames in first replica (17330). Warning: RemdTraj: Replica ../traj.2.15 frames (17331) does not match Warning: # frames in first replica (17330). [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 out rmsd_ensemble.dat ] 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 ------------------------------------------------- INPUT ENSEMBLE: Ensemble size is 18 Ensemble Temperature Map: 280.00 -> 0 286.04 -> 1 292.18 -> 2 298.41 -> 3 304.74 -> 4 311.17 -> 5 317.69 -> 6 324.31 -> 7 331.03 -> 8 337.85 -> 9 344.79 -> 10 351.82 -> 11 358.97 -> 12 366.22 -> 13 373.59 -> 14 381.07 -> 15 388.67 -> 16 396.40 -> 17 INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 100 of 50000) Processing ensemble using replica temperatures 1: REMD trajectories (18 total), lowest replica 'traj.2.01' (reading 100 of 17330) Processing ensemble using replica temperatures Coordinate processing will occur on 200 frames. PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 200 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol REFERENCE FRAMES (1 total): 0: '../../../../aa-A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 ENSEMBLE OUTPUT TRAJECTORIES (Numerical filename suffix corresponds to above map): TIME: Run Initialization took 0.6598 seconds. BEGIN ENSEMBLE 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 out rmsd_ensemble.dat ] 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 (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.2.01 (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. Read 200 frames and processed 200 frames. TIME: Trajectory processing: 2.3728 s TIME: Avg. throughput= 84.2879 frames / second. ENSEMBLE ACTION OUTPUT: DATASETS: 19 data sets: [a-form]:1%0 "[a-form]:1" (reference), size is 1 '../../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform%0 "rms_2_aform" (double, rms), size is 200 rms_2_aform%1 "rms_2_aform%1" (double, rms), size is 200 rms_2_aform%2 "rms_2_aform%2" (double, rms), size is 200 rms_2_aform%3 "rms_2_aform%3" (double, rms), size is 200 rms_2_aform%4 "rms_2_aform%4" (double, rms), size is 200 rms_2_aform%5 "rms_2_aform%5" (double, rms), size is 200 rms_2_aform%6 "rms_2_aform%6" (double, rms), size is 200 rms_2_aform%7 "rms_2_aform%7" (double, rms), size is 200 rms_2_aform%8 "rms_2_aform%8" (double, rms), size is 200 rms_2_aform%9 "rms_2_aform%9" (double, rms), size is 200 rms_2_aform%10 "rms_2_aform%10" (double, rms), size is 200 rms_2_aform%11 "rms_2_aform%11" (double, rms), size is 200 rms_2_aform%12 "rms_2_aform%12" (double, rms), size is 200 rms_2_aform%13 "rms_2_aform%13" (double, rms), size is 200 rms_2_aform%14 "rms_2_aform%14" (double, rms), size is 200 rms_2_aform%15 "rms_2_aform%15" (double, rms), size is 200 rms_2_aform%16 "rms_2_aform%16" (double, rms), size is 200 rms_2_aform%17 "rms_2_aform%17" (double, rms), size is 200 DATAFILES: rmsd_ensemble.dat (Standard Data File): rms_2_aform rms_2_aform%1 rms_2_aform%2 rms_2_aform%3 ... rms_2_aform%14 rms_2_aform%15 rms_2_aform%16 rms_2_aform%17 ---------- RUN END --------------------------------------------------- [hist rms_2_aform%1,0,5,0.1 out hist_rmsd-all_1000ns.agr norm] Hist: hist_rmsd-all_1000ns.agr: Set up for 1 dimensions using the following datasets: [ rms_2_aform%1 ] norm: Sum over bins will be normalized to 1.0. [hist rms_2_aform%2,0,5,0.1 out hist_rmsd-all_1000ns.agr norm] Hist: hist_rmsd-all_1000ns.agr: Set up for 1 dimensions using the following datasets: [ rms_2_aform%2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 2 analyses: 0: [hist rms_2_aform%1,0,5,0.1 out hist_rmsd-all_1000ns.agr norm] Dim rms_2_aform%1: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 200 data points in each dimension. Hist: Allocating histogram, total bins = 50 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 200.000000 1: [hist rms_2_aform%2,0,5,0.1 out hist_rmsd-all_1000ns.agr norm] Dim rms_2_aform%2: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 200 data points in each dimension. Hist: Allocating histogram, total bins = 50 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 200.000000 TIME: Analyses took 0.0001 seconds. DATASETS: 21 data sets: [a-form]:1%0 "[a-form]:1" (reference), size is 1 '../../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform%0 "rms_2_aform" (double, rms), size is 200 rms_2_aform%1 "rms_2_aform%1" (double, rms), size is 200 rms_2_aform%2 "rms_2_aform%2" (double, rms), size is 200 rms_2_aform%3 "rms_2_aform%3" (double, rms), size is 200 rms_2_aform%4 "rms_2_aform%4" (double, rms), size is 200 rms_2_aform%5 "rms_2_aform%5" (double, rms), size is 200 rms_2_aform%6 "rms_2_aform%6" (double, rms), size is 200 rms_2_aform%7 "rms_2_aform%7" (double, rms), size is 200 rms_2_aform%8 "rms_2_aform%8" (double, rms), size is 200 rms_2_aform%9 "rms_2_aform%9" (double, rms), size is 200 rms_2_aform%10 "rms_2_aform%10" (double, rms), size is 200 rms_2_aform%11 "rms_2_aform%11" (double, rms), size is 200 rms_2_aform%12 "rms_2_aform%12" (double, rms), size is 200 rms_2_aform%13 "rms_2_aform%13" (double, rms), size is 200 rms_2_aform%14 "rms_2_aform%14" (double, rms), size is 200 rms_2_aform%15 "rms_2_aform%15" (double, rms), size is 200 rms_2_aform%16 "rms_2_aform%16" (double, rms), size is 200 rms_2_aform%17 "rms_2_aform%17" (double, rms), size is 200 Hist_00019%17 "Hist_00019%17" (double), size is 50 Hist_00020%17 "Hist_00020%17" (double), size is 50 DATAFILES: rmsd_ensemble.dat (Standard Data File): rms_2_aform rms_2_aform%1 rms_2_aform%2 rms_2_aform%3 ... rms_2_aform%14 rms_2_aform%15 rms_2_aform%16 rms_2_aform%17 hist_rmsd-all_1000ns.agr (Grace File): Hist_00019%17 Hist_00020%17 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 6.3634 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.