CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 07/29/16 11:52:43
| Available memory: 15.934 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= 89.7887 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 : 556.8629 s (100.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0091 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 556.8721 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= 88.6594 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 0.0418 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 : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 563.9558 s ( 99.95%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0418 s ( 0.01%)
TIME: Data File Write : 0.2620 s ( 0.05%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 564.2597 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1121.6141 seconds.
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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.