CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/21/16 12:26:30
| Available memory: 3.358 GB
INPUT: Reading input from 'pt-analysis.chi-py-pu.in'
[parm ../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apa]]
Reading '../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apg]]
Reading '../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpa]]
Reading '../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpg]]
Reading '../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apc]]
Reading '../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apu]]
Reading '../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpc]]
Reading '../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpu]]
Reading '../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpa]]
Reading '../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpg]]
Reading '../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upa]]
Reading '../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upg]]
Reading '../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpc]]
Reading '../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpu]]
Reading '../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upc]]
Reading '../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upu]]
Reading '../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[trajin ../../ca/cluster-all/km-6/ctraj.c2 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c2' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c2 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c2' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c1 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c1' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c1 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c1' as Amber NetCDF
[dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2]
Output range is -180 to 180 degrees.
[dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4]
Output range is -180 to 180 degrees.
[dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3']
Output range is -180 to 180 degrees.
[dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P]
Output range is -180 to 180 degrees.
[dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5']
Output range is -180 to 180 degrees.
[dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5']
Output range is -180 to 180 degrees.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (16 total):
0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (4 total):
0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741)
1: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719)
2: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590)
3: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072)
Coordinate processing will occur on 144122 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions):
0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
[:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
[:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
[:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
[:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
----- ctraj.c2 (1-88741, 1) -----
0% 10% 20% 30% 40% 50% 60%
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions):
0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
[:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
[:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
[:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
[:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
----- ctraj.c2 (1-17719, 1) -----
70%
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions):
0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
[:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
[:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
[:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
[:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
----- ctraj.c1 (1-18590, 1) -----
80%
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions):
0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
[:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
[:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
[:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
[:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
----- ctraj.c1 (1-19072, 1) -----
90% 100% Complete.
Read 144122 frames and processed 144122 frames.
TIME: Avg. throughput= 296651.0919 frames / second.
ACTION OUTPUT:
DATASETS (6 total):
c1 "c1" (double, torsion(chin)), size is 144122
c2 "c2" (double, torsion(chin)), size is 144122
d1 "d1" (double, torsion(delta)), size is 144122
e1 "e1" (double, torsion(epsilon)), size is 144122
z1 "z1" (double, torsion(zeta)), size is 144122
a2 "a2" (double, torsion(alpha)), size is 144122
RUN TIMING:
TIME: Init : 0.0001 s ( 0.02%)
TIME: Trajectory Process : 0.4858 s ( 99.97%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.4860 s
---------- RUN END ---------------------------------------------------
[hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yu.gnu norm]
Hist: 2dhist_c1_c2_yu.gnu: Set up for 2 dimensions using the following datasets:
[ c1 c2 ]
norm: Sum over bins will be normalized to 1.0.
[hist d1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_d1_c2_yu.gnu norm]
Hist: 2dhist_d1_c2_yu.gnu: Set up for 2 dimensions using the following datasets:
[ d1 c2 ]
norm: Sum over bins will be normalized to 1.0.
[hist z1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_z1_c2_yu.gnu norm]
Hist: 2dhist_z1_c2_yu.gnu: Set up for 2 dimensions using the following datasets:
[ z1 c2 ]
norm: Sum over bins will be normalized to 1.0.
[hist a2,-180,180,0.5 c2,-180,180,0.5 out 2dhist_a2_c2_yu.gnu norm]
Hist: 2dhist_a2_c2_yu.gnu: Set up for 2 dimensions using the following datasets:
[ a2 c2 ]
norm: Sum over bins will be normalized to 1.0.
[hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2_yu.gnu norm]
Hist: 2dhist_z1_a2_yu.gnu: Set up for 2 dimensions using the following datasets:
[ z1 a2 ]
norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (16 total):
0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (4 total):
0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741)
1: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719)
2: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590)
3: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072)
Coordinate processing will occur on 144122 frames.
BEGIN TRAJECTORY PROCESSING:
----- ctraj.c2 (1-88741, 1) -----
0% 10% 20% 30% 40% 50% 60%
----- ctraj.c2 (1-17719, 1) -----
70%
----- ctraj.c1 (1-18590, 1) -----
80%
----- ctraj.c1 (1-19072, 1) -----
90% 100% Complete.
Read 144122 frames and processed 144122 frames.
TIME: Avg. throughput= 541573.8190 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 5 analyses:
0: [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yu.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim c1: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=-180 max=180 step=0.5.
Dim c2: -180.000000->180.000000, step 0.500000, 720 bins.
Hist: 144122 data points in each dimension.
Hist: Allocating histogram, total bins = 518400
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 144122
1: [hist d1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_d1_c2_yu.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim d1: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=-180 max=180 step=0.5.
Dim c2: -180.000000->180.000000, step 0.500000, 720 bins.
Hist: 144122 data points in each dimension.
Hist: Allocating histogram, total bins = 518400
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 144122
2: [hist z1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_z1_c2_yu.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim z1: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=-180 max=180 step=0.5.
Dim c2: -180.000000->180.000000, step 0.500000, 720 bins.
Hist: 144122 data points in each dimension.
Hist: Allocating histogram, total bins = 518400
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 144122
3: [hist a2,-180,180,0.5 c2,-180,180,0.5 out 2dhist_a2_c2_yu.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim a2: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=-180 max=180 step=0.5.
Dim c2: -180.000000->180.000000, step 0.500000, 720 bins.
Hist: 144122 data points in each dimension.
Hist: Allocating histogram, total bins = 518400
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 144122
4: [hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2_yu.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim z1: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=-180 max=180 step=0.5.
Dim a2: -180.000000->180.000000, step 0.500000, 720 bins.
Hist: 144122 data points in each dimension.
Hist: Allocating histogram, total bins = 518400
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 144122
TIME: Analyses took 0.0508 seconds.
DATASETS (11 total):
c1 "c1" (double, torsion(chin)), size is 144122
c2 "c2" (double, torsion(chin)), size is 144122
d1 "d1" (double, torsion(delta)), size is 144122
e1 "e1" (double, torsion(epsilon)), size is 144122
z1 "z1" (double, torsion(zeta)), size is 144122
a2 "a2" (double, torsion(alpha)), size is 144122
Hist_00022 "Hist_00022" (double matrix), size is 518400
Hist_00023 "Hist_00023" (double matrix), size is 518400
Hist_00024 "Hist_00024" (double matrix), size is 518400
Hist_00025 "Hist_00025" (double matrix), size is 518400
Hist_00026 "Hist_00026" (double matrix), size is 518400
DATAFILES (5 total):
2dhist_c1_c2_yu.gnu (Gnuplot File): Hist_00022
2dhist_d1_c2_yu.gnu (Gnuplot File): Hist_00023
2dhist_z1_c2_yu.gnu (Gnuplot File): Hist_00024
2dhist_a2_c2_yu.gnu (Gnuplot File): Hist_00025
2dhist_z1_a2_yu.gnu (Gnuplot File): Hist_00026
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 0.2661 s ( 4.54%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0508 s ( 0.87%)
TIME: Data File Write : 5.5498 s ( 94.58%)
TIME: Other : 0.0011 s ( 0.00%)
TIME: Run Total 5.8678 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 6.4194 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.