CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/22/16 13:17:49
| Available memory: 1.657 GB

INPUT: Reading input from 'pt-analysis1.in'
  [parm ../noWAt.topo.hmr]
	Reading '../noWAt.topo.hmr' as Amber Topology
  [trajin ../ctraj.c1]
	Reading '../ctraj.c1' as Amber NetCDF
  [reference ../../../../aa/A-form.pdb [a-form]]
	Reading '../../../../aa/A-form.pdb' as PDB
	Setting active reference for distance-based masks: 'A-form.pdb'
  [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
    RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [distance dist_sugar_ox :1@O2' :2@O4']
    DISTANCE: :1@O2' to :2@O4', center of mass.
  [distance dist_N3-O5p :1@N3 :1@O5']
    DISTANCE: :1@N3 to :1@O5', center of mass.
  [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass.
  [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
    DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3']
              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 c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi]
    DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4]
              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.
  [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
    DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4']
              Output range is -180 to 180 degrees.
  [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
    DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3']
              Output range is -180 to 180 degrees.
  [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
    DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3']
              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.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 162772 of 162772)
  Coordinate processing will occur on 162772 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions):
  0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
	Target mask: [:1,2&!@H*](41)
	Reference 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.
  1: [distance dist_sugar_ox :1@O2' :2@O4']
	:1@O2' (1 atoms) to :2@O4' (1 atoms), imaged.
  2: [distance dist_N3-O5p :1@N3 :1@O5']
	:1@N3 (1 atoms) to :1@O5' (1 atoms), imaged.
  3: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
  4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
	 [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1)
  5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
	 [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
  6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
	 [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
  7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
	 [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
  8: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1)
  9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
	 [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
  10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
	 [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1)
  11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
	 [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1)
  12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
	 [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1)
  13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c1 (1-162772, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 162772 frames and processed 162772 frames.
TIME: Avg. throughput= 172449.1569 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 162772
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 162772
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 162772
	COM "COM" (double, distance), size is 162772
	g1 "g1" (double, torsion(gamma)), size is 162772
	d1 "d1" (double, torsion(delta)), size is 162772
	e1 "e1" (double, torsion(epsilon)), size is 162772
	z1 "z1" (double, torsion(zeta)), size is 162772
	c1 "c1" (double, torsion(chin)), size is 162772
	a2 "a2" (double, torsion(alpha)), size is 162772
	b2 "b2" (double, torsion(beta)), size is 162772
	g2 "g2" (double, torsion(gamma)), size is 162772
	d2 "d2" (double, torsion(delta)), size is 162772
	c2 "c2" (double, torsion(chin)), size is 162772

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.9439 s ( 99.98%)
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 0.9440 s
---------- RUN END ---------------------------------------------------
  [avg rms_2_aform out avg-rmsd-all.dat]
    AVERAGE: Calculating average of 1 data sets.
	Data set base name 'AVERAGE_00016'
	Output to to 'avg-rmsd-all.dat'
  [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
	Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets:
	[ rms_2_aform ]
	norm: Sum over bins will be normalized to 1.0.
  [hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
	Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets:
	[ COM ]
	norm: Sum over bins will be normalized to 1.0.
  [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
	Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets:
	[ dist_sugar_ox ]
	norm: Sum over bins will be normalized to 1.0.
  [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
	Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets:
	[ dist_N3-O5p ]
	norm: Sum over bins will be normalized to 1.0.
  [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
	Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets:
	[ rms_2_aform dist_sugar_ox ]
	norm: Sum over bins will be normalized to 1.0.
  [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm]
	Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ g1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
	Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ d1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
	Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ e1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
	Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ z1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
	Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets:
	[ c1 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
	Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ a2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
	Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ b2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
	Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ g2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
	Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ d2 ]
	norm: Sum over bins will be normalized to 1.0.
  [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
	Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets:
	[ c2 ]
	norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 162772 of 162772)
  Coordinate processing will occur on 162772 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c1 (1-162772, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 162772 frames and processed 162772 frames.
TIME: Avg. throughput= 696887.4427 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 16 analyses:
  0: [avg rms_2_aform out avg-rmsd-all.dat]
	1: rms_2_aform
  1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
		Calculating bins from min=0 max=5 step=0.1.
	Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
	Hist: 162772 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 162772
  2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim COM: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 1838 Coordinates out of bounds (-1)
	Warning: Frame 2998 Coordinates out of bounds (-1)
	Warning: Frame 4189 Coordinates out of bounds (-1)
	Warning: Frame 4522 Coordinates out of bounds (-1)
	Warning: Frame 5997 Coordinates out of bounds (-1)
	Warning: Frame 6175 Coordinates out of bounds (-1)
	Warning: Frame 8492 Coordinates out of bounds (-1)
	Warning: Frame 11314 Coordinates out of bounds (-1)
	Warning: Frame 17336 Coordinates out of bounds (-1)
	Warning: Frame 18492 Coordinates out of bounds (-1)
	Warning: Frame 20790 Coordinates out of bounds (-1)
	Warning: Frame 24631 Coordinates out of bounds (-1)
	Warning: Frame 28573 Coordinates out of bounds (-1)
	Warning: Frame 29288 Coordinates out of bounds (-1)
	Warning: Frame 29937 Coordinates out of bounds (-1)
	Warning: Frame 32566 Coordinates out of bounds (-1)
	Warning: Frame 32867 Coordinates out of bounds (-1)
	Warning: Frame 33424 Coordinates out of bounds (-1)
	Warning: Frame 34848 Coordinates out of bounds (-1)
	Warning: Frame 35624 Coordinates out of bounds (-1)
	Warning: Frame 37842 Coordinates out of bounds (-1)
	Warning: Frame 42420 Coordinates out of bounds (-1)
	Warning: Frame 42610 Coordinates out of bounds (-1)
	Warning: Frame 47902 Coordinates out of bounds (-1)
	Warning: Frame 48409 Coordinates out of bounds (-1)
	Warning: Frame 49424 Coordinates out of bounds (-1)
	Warning: Frame 49554 Coordinates out of bounds (-1)
	Warning: Frame 56400 Coordinates out of bounds (-1)
	Warning: Frame 57647 Coordinates out of bounds (-1)
	Warning: Frame 60378 Coordinates out of bounds (-1)
	Warning: Frame 61223 Coordinates out of bounds (-1)
	Warning: Frame 62344 Coordinates out of bounds (-1)
	Warning: Frame 62374 Coordinates out of bounds (-1)
	Warning: Frame 63740 Coordinates out of bounds (-1)
	Warning: Frame 64286 Coordinates out of bounds (-1)
	Warning: Frame 66094 Coordinates out of bounds (-1)
	Warning: Frame 66261 Coordinates out of bounds (-1)
	Warning: Frame 66589 Coordinates out of bounds (-1)
	Warning: Frame 67146 Coordinates out of bounds (-1)
	Warning: Frame 67754 Coordinates out of bounds (-1)
	Warning: Frame 67884 Coordinates out of bounds (-1)
	Warning: Frame 67990 Coordinates out of bounds (-1)
	Warning: Frame 68522 Coordinates out of bounds (-1)
	Warning: Frame 70633 Coordinates out of bounds (-1)
	Warning: Frame 70704 Coordinates out of bounds (-1)
	Warning: Frame 70787 Coordinates out of bounds (-1)
	Warning: Frame 71366 Coordinates out of bounds (-1)
	Warning: Frame 71659 Coordinates out of bounds (-1)
	Warning: Frame 72097 Coordinates out of bounds (-1)
	Warning: Frame 72544 Coordinates out of bounds (-1)
	Warning: Frame 73148 Coordinates out of bounds (-1)
	Warning: Frame 73230 Coordinates out of bounds (-1)
	Warning: Frame 74176 Coordinates out of bounds (-1)
	Warning: Frame 75057 Coordinates out of bounds (-1)
	Warning: Frame 75071 Coordinates out of bounds (-1)
	Warning: Frame 75883 Coordinates out of bounds (-1)
	Warning: Frame 76361 Coordinates out of bounds (-1)
	Warning: Frame 76362 Coordinates out of bounds (-1)
	Warning: Frame 76369 Coordinates out of bounds (-1)
	Warning: Frame 76889 Coordinates out of bounds (-1)
	Warning: Frame 76893 Coordinates out of bounds (-1)
	Warning: Frame 77685 Coordinates out of bounds (-1)
	Warning: Frame 78967 Coordinates out of bounds (-1)
	Warning: Frame 80036 Coordinates out of bounds (-1)
	Warning: Frame 80692 Coordinates out of bounds (-1)
	Warning: Frame 81581 Coordinates out of bounds (-1)
	Warning: Frame 81728 Coordinates out of bounds (-1)
	Warning: Frame 81827 Coordinates out of bounds (-1)
	Warning: Frame 82249 Coordinates out of bounds (-1)
	Warning: Frame 82669 Coordinates out of bounds (-1)
	Warning: Frame 82684 Coordinates out of bounds (-1)
	Warning: Frame 82955 Coordinates out of bounds (-1)
	Warning: Frame 92689 Coordinates out of bounds (-1)
	Warning: Frame 115737 Coordinates out of bounds (-1)
	Warning: Frame 117098 Coordinates out of bounds (-1)
	Warning: Frame 120144 Coordinates out of bounds (-1)
	Warning: Frame 120242 Coordinates out of bounds (-1)
	Warning: Frame 120537 Coordinates out of bounds (-1)
	Warning: Frame 121694 Coordinates out of bounds (-1)
	Warning: Frame 121855 Coordinates out of bounds (-1)
	Warning: Frame 122887 Coordinates out of bounds (-1)
	Warning: Frame 123885 Coordinates out of bounds (-1)
	Warning: Frame 125091 Coordinates out of bounds (-1)
	Warning: Frame 126661 Coordinates out of bounds (-1)
	Warning: Frame 127780 Coordinates out of bounds (-1)
	Warning: Frame 128118 Coordinates out of bounds (-1)
	Warning: Frame 128222 Coordinates out of bounds (-1)
	Warning: Frame 128235 Coordinates out of bounds (-1)
	Warning: Frame 129098 Coordinates out of bounds (-1)
	Warning: Frame 130302 Coordinates out of bounds (-1)
	Warning: Frame 130563 Coordinates out of bounds (-1)
	Warning: Frame 130617 Coordinates out of bounds (-1)
	Warning: Frame 136173 Coordinates out of bounds (-1)
	Warning: Frame 137997 Coordinates out of bounds (-1)
	Warning: Frame 138469 Coordinates out of bounds (-1)
	Warning: Frame 140802 Coordinates out of bounds (-1)
	Warning: Frame 146178 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162675
  3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 162772 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 162772
  4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 162772 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 162772
  5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
		Calculating bins from min=0 max=5 step=0.1.
	Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
		Calculating bins from min=0 max=10 step=0.1.
	Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 5000
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  6: [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim g1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim d1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim e1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim z1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim c1: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim a2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim b2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim g2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim d2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772
  15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
		Calculating bins from min=-180 max=180 step=1.
	Dim c2: -180.000000->180.000000, step 1.000000, 360 bins.
	Hist: 162772 data points in each dimension.
	Hist: Allocating histogram, total bins = 360
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 162772

TIME: Analyses took 0.0342 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 162772
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 162772
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 162772
	COM "COM" (double, distance), size is 162772
	g1 "g1" (double, torsion(gamma)), size is 162772
	d1 "d1" (double, torsion(delta)), size is 162772
	e1 "e1" (double, torsion(epsilon)), size is 162772
	z1 "z1" (double, torsion(zeta)), size is 162772
	c1 "c1" (double, torsion(chin)), size is 162772
	a2 "a2" (double, torsion(alpha)), size is 162772
	b2 "b2" (double, torsion(beta)), size is 162772
	g2 "g2" (double, torsion(gamma)), size is 162772
	d2 "d2" (double, torsion(delta)), size is 162772
	c2 "c2" (double, torsion(chin)), size is 162772
	AVERAGE_00016[avg] "AVERAGE_00016[avg]" (double), size is 1
	AVERAGE_00016[sd] "AVERAGE_00016[sd]" (double), size is 1
	AVERAGE_00016[ymin] "AVERAGE_00016[ymin]" (double), size is 1
	AVERAGE_00016[ymax] "AVERAGE_00016[ymax]" (double), size is 1
	AVERAGE_00016[yminidx] "AVERAGE_00016[yminidx]" (integer), size is 1
	AVERAGE_00016[ymaxidx] "AVERAGE_00016[ymaxidx]" (integer), size is 1
	AVERAGE_00016[names] "AVERAGE_00016[names]" (string), size is 1
	RMSD "RMSD" (double), size is 50
	CoM "CoM" (double), size is 100
	Hist_00025 "Hist_00025" (double), size is 100
	Hist_00026 "Hist_00026" (double), size is 100
	Hist_00027 "Hist_00027" (double matrix), size is 5000
	gamma_1 "gamma_1" (double), size is 360
	delta_1 "delta_1" (double), size is 360
	epsilon_1 "epsilon_1" (double), size is 360
	zeta_1 "zeta_1" (double), size is 360
	chi_1 "chi_1" (double), size is 360
	alpha_2 "alpha_2" (double), size is 360
	beta_2 "beta_2" (double), size is 360
	gamma_2 "gamma_2" (double), size is 360
	delta_2 "delta_2" (double), size is 360
	chi_2 "chi_2" (double), size is 360

DATAFILES (15 total):
  avg-rmsd-all.dat (Standard Data File):  AVERAGE_00016[avg] AVERAGE_00016[sd] AVERAGE_00016[ymin] AVERAGE_00016[ymax] AVERAGE_00016[yminidx] AVERAGE_00016[ymaxidx] AVERAGE_00016[names]
  rmsd-hist.dat (Standard Data File):  RMSD
  COM-hist.dat (Standard Data File):  CoM
  distO2O4-hist.dat (Standard Data File):  Hist_00025
  distN3-O5p-hist.dat (Standard Data File):  Hist_00026
  2dhist_rms-dist.gnu (Gnuplot File):  Hist_00027
  dihed_a2-hist.dat (Standard Data File):  gamma_1 alpha_2
  dihed_d1-hist.dat (Standard Data File):  delta_1
  dihed_e1-hist.dat (Standard Data File):  epsilon_1
  dihed_z1-hist.dat (Standard Data File):  zeta_1
  dihed_c1-hist.dat (Standard Data File):  chi_1
  dihed_b2-hist.dat (Standard Data File):  beta_2
  dihed_g2-hist.dat (Standard Data File):  gamma_2
  dihed_d2-hist.dat (Standard Data File):  delta_2
  dihed_c2-hist.dat (Standard Data File):  chi_2

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.04%)
TIME:		Trajectory Process : 0.2336 s ( 81.24%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0342 s ( 11.88%)
TIME:		Data File Write    : 0.0196 s (  6.82%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 0.2875 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.2443 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.