CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 07/29/16 11:53:59 | Available memory: 66.440 GB INPUT: Reading input from 'pt-test-O5N3.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [autoimage origin] Warning: Action specified before trajin/ensemble. Assuming trajin. AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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] Reading '../../traj.1.01' as Amber NetCDF [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [distance N3HO5p :1@N3 :1@HO5'] DISTANCE: :1@N3 to :1@HO5', center of mass. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 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. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (3 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 2: [distance N3HO5p :1@N3 :1@HO5'] :1@N3 (1 atoms) to :1@HO5' (1 atoms), imaged. ----- 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: Avg. throughput= 83.6244 frames / second. ACTION OUTPUT: DATASETS (1 total): N3HO5p "N3HO5p" (double, distance), size is 50000 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 597.9119 s (100.00%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 597.9120 s ---------- RUN END --------------------------------------------------- [hist N3HO5p,0,10,0.1 out ./298.41/dist_N3-HO5p.dat norm] Hist: ./298.41/dist_N3-HO5p.dat: Set up for 1 dimensions using the following datasets: [ N3HO5p ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 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. BEGIN TRAJECTORY PROCESSING: ----- 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: Avg. throughput= 915.2720 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [hist N3HO5p,0,10,0.1 out ./298.41/dist_N3-HO5p.dat norm] Calculating bins from min=0 max=10 step=0.1. Dim N3HO5p: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 100 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 TIME: Analyses took 0.0008 seconds. DATASETS (2 total): N3HO5p "N3HO5p" (double, distance), size is 50000 Hist_00002 "Hist_00002" (double), size is 100 DATAFILES (1 total): dist_N3-HO5p.dat (Standard Data File): Hist_00002 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 54.6286 s ( 99.96%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0008 s ( 0.00%) TIME: Data File Write : 0.0210 s ( 0.04%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 54.6504 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 652.9924 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.