CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 11:39:56
| Available memory: 1.900 GB

INPUT: Reading input from 'pt-analysis1.in'
  [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr]
	Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [trajin ../ctraj.c0]
	Reading '../ctraj.c0' as Amber NetCDF
  [reference ../../../A-form.pdb [a-form]]
	Reading '../../../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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, 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@N1 :1@C2 type chi]
    DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2]
              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@N1 :2@C2 type chi]
    DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2]
              Output range is -180 to 180 degrees.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 224808 of 224808)
  Coordinate processing will occur on 224808 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*](37)
	Reference mask: [:1,2&!@H*](37)
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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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@N1 :1@C2 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](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@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c0 (1-224808, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 224808 frames and processed 224808 frames.
TIME: Avg. throughput= 130999.5117 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 224808
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 224808
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 224808
	COM "COM" (double, distance), size is 224808
	g1 "g1" (double, torsion(gamma)), size is 224808
	d1 "d1" (double, torsion(delta)), size is 224808
	e1 "e1" (double, torsion(epsilon)), size is 224808
	z1 "z1" (double, torsion(zeta)), size is 224808
	c1 "c1" (double, torsion(chin)), size is 224808
	a2 "a2" (double, torsion(alpha)), size is 224808
	b2 "b2" (double, torsion(beta)), size is 224808
	g2 "g2" (double, torsion(gamma)), size is 224808
	d2 "d2" (double, torsion(delta)), size is 224808
	c2 "c2" (double, torsion(chin)), size is 224808

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.00%)
TIME:		Trajectory Process : 1.7161 s ( 99.99%)
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 1.7162 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_g1-hist.dat name gamma_1 norm]
	Hist: dihed_g1-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, 59 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 224808 of 224808)
  Coordinate processing will occur on 224808 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c0 (1-224808, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 224808 frames and processed 224808 frames.
TIME: Avg. throughput= 740798.8348 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: 224808 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 224808
  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: 224808 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 2671 Coordinates out of bounds (-1)
	Warning: Frame 2947 Coordinates out of bounds (-1)
	Warning: Frame 3334 Coordinates out of bounds (-1)
	Warning: Frame 9286 Coordinates out of bounds (-1)
	Warning: Frame 15954 Coordinates out of bounds (-1)
	Warning: Frame 26109 Coordinates out of bounds (-1)
	Warning: Frame 28538 Coordinates out of bounds (-1)
	Warning: Frame 31372 Coordinates out of bounds (-1)
	Warning: Frame 36027 Coordinates out of bounds (-1)
	Warning: Frame 41199 Coordinates out of bounds (-1)
	Warning: Frame 45996 Coordinates out of bounds (-1)
	Warning: Frame 49110 Coordinates out of bounds (-1)
	Warning: Frame 61602 Coordinates out of bounds (-1)
	Warning: Frame 63078 Coordinates out of bounds (-1)
	Warning: Frame 65878 Coordinates out of bounds (-1)
	Warning: Frame 73121 Coordinates out of bounds (-1)
	Warning: Frame 76071 Coordinates out of bounds (-1)
	Warning: Frame 83486 Coordinates out of bounds (-1)
	Warning: Frame 89393 Coordinates out of bounds (-1)
	Warning: Frame 90849 Coordinates out of bounds (-1)
	Warning: Frame 91958 Coordinates out of bounds (-1)
	Warning: Frame 95230 Coordinates out of bounds (-1)
	Warning: Frame 95611 Coordinates out of bounds (-1)
	Warning: Frame 96254 Coordinates out of bounds (-1)
	Warning: Frame 97375 Coordinates out of bounds (-1)
	Warning: Frame 101864 Coordinates out of bounds (-1)
	Warning: Frame 102020 Coordinates out of bounds (-1)
	Warning: Frame 102519 Coordinates out of bounds (-1)
	Warning: Frame 106273 Coordinates out of bounds (-1)
	Warning: Frame 106391 Coordinates out of bounds (-1)
	Warning: Frame 106596 Coordinates out of bounds (-1)
	Warning: Frame 109614 Coordinates out of bounds (-1)
	Warning: Frame 109627 Coordinates out of bounds (-1)
	Warning: Frame 110341 Coordinates out of bounds (-1)
	Warning: Frame 113545 Coordinates out of bounds (-1)
	Warning: Frame 114110 Coordinates out of bounds (-1)
	Warning: Frame 115371 Coordinates out of bounds (-1)
	Warning: Frame 115549 Coordinates out of bounds (-1)
	Warning: Frame 115872 Coordinates out of bounds (-1)
	Warning: Frame 116182 Coordinates out of bounds (-1)
	Warning: Frame 116413 Coordinates out of bounds (-1)
	Warning: Frame 116731 Coordinates out of bounds (-1)
	Warning: Frame 117707 Coordinates out of bounds (-1)
	Warning: Frame 118984 Coordinates out of bounds (-1)
	Warning: Frame 119209 Coordinates out of bounds (-1)
	Warning: Frame 119234 Coordinates out of bounds (-1)
	Warning: Frame 120138 Coordinates out of bounds (-1)
	Warning: Frame 120705 Coordinates out of bounds (-1)
	Warning: Frame 120976 Coordinates out of bounds (-1)
	Warning: Frame 120977 Coordinates out of bounds (-1)
	Warning: Frame 121008 Coordinates out of bounds (-1)
	Warning: Frame 121346 Coordinates out of bounds (-1)
	Warning: Frame 121364 Coordinates out of bounds (-1)
	Warning: Frame 121927 Coordinates out of bounds (-1)
	Warning: Frame 121977 Coordinates out of bounds (-1)
	Warning: Frame 122052 Coordinates out of bounds (-1)
	Warning: Frame 122361 Coordinates out of bounds (-1)
	Warning: Frame 122694 Coordinates out of bounds (-1)
	Warning: Frame 122970 Coordinates out of bounds (-1)
	Warning: Frame 122978 Coordinates out of bounds (-1)
	Warning: Frame 123882 Coordinates out of bounds (-1)
	Warning: Frame 123958 Coordinates out of bounds (-1)
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	Warning: Frame 124810 Coordinates out of bounds (-1)
	Warning: Frame 124882 Coordinates out of bounds (-1)
	Warning: Frame 124931 Coordinates out of bounds (-1)
	Warning: Frame 125006 Coordinates out of bounds (-1)
	Warning: Frame 125403 Coordinates out of bounds (-1)
	Warning: Frame 125439 Coordinates out of bounds (-1)
	Warning: Frame 126188 Coordinates out of bounds (-1)
	Warning: Frame 126293 Coordinates out of bounds (-1)
	Warning: Frame 126571 Coordinates out of bounds (-1)
	Warning: Frame 126700 Coordinates out of bounds (-1)
	Warning: Frame 127177 Coordinates out of bounds (-1)
	Warning: Frame 128529 Coordinates out of bounds (-1)
	Warning: Frame 128711 Coordinates out of bounds (-1)
	Warning: Frame 128798 Coordinates out of bounds (-1)
	Warning: Frame 128938 Coordinates out of bounds (-1)
	Warning: Frame 129209 Coordinates out of bounds (-1)
	Warning: Frame 130383 Coordinates out of bounds (-1)
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	Warning: Frame 130757 Coordinates out of bounds (-1)
	Warning: Frame 130976 Coordinates out of bounds (-1)
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	Warning: Frame 131188 Coordinates out of bounds (-1)
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	Warning: Frame 131611 Coordinates out of bounds (-1)
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	Warning: Frame 131791 Coordinates out of bounds (-1)
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	Warning: Frame 132247 Coordinates out of bounds (-1)
	Warning: Frame 132460 Coordinates out of bounds (-1)
	Warning: Frame 132686 Coordinates out of bounds (-1)
	Warning: Frame 132791 Coordinates out of bounds (-1)
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	Warning: Frame 133156 Coordinates out of bounds (-1)
	Warning: Frame 133221 Coordinates out of bounds (-1)
	Warning: Frame 133569 Coordinates out of bounds (-1)
	Warning: Frame 133914 Coordinates out of bounds (-1)
	Warning: Frame 134157 Coordinates out of bounds (-1)
	Warning: Frame 134377 Coordinates out of bounds (-1)
	Warning: Frame 134385 Coordinates out of bounds (-1)
	Warning: Frame 136733 Coordinates out of bounds (-1)
	Warning: Frame 140029 Coordinates out of bounds (-1)
	Warning: Frame 142557 Coordinates out of bounds (-1)
	Warning: Frame 144388 Coordinates out of bounds (-1)
	Warning: Frame 147477 Coordinates out of bounds (-1)
	Warning: Frame 147576 Coordinates out of bounds (-1)
	Warning: Frame 152130 Coordinates out of bounds (-1)
	Warning: Frame 154595 Coordinates out of bounds (-1)
	Warning: Frame 158775 Coordinates out of bounds (-1)
	Warning: Frame 159844 Coordinates out of bounds (-1)
	Warning: Frame 163247 Coordinates out of bounds (-1)
	Warning: Frame 163986 Coordinates out of bounds (-1)
	Warning: Frame 165132 Coordinates out of bounds (-1)
	Warning: Frame 169035 Coordinates out of bounds (-1)
	Warning: Frame 171643 Coordinates out of bounds (-1)
	Warning: Frame 172594 Coordinates out of bounds (-1)
	Warning: Frame 174487 Coordinates out of bounds (-1)
	Warning: Frame 174661 Coordinates out of bounds (-1)
	Warning: Frame 175467 Coordinates out of bounds (-1)
	Warning: Frame 189078 Coordinates out of bounds (-1)
	Warning: Frame 193437 Coordinates out of bounds (-1)
	Warning: Frame 202584 Coordinates out of bounds (-1)
	Warning: Frame 202586 Coordinates out of bounds (-1)
	Warning: Frame 207584 Coordinates out of bounds (-1)
	Warning: Frame 213902 Coordinates out of bounds (-1)
	Warning: Frame 219692 Coordinates out of bounds (-1)
	Warning: Frame 220261 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 224678
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  6: [hist g1,-180,180,1 out dihed_g1-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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808
  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: 224808 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 224808

TIME: Analyses took 0.0421 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 224808
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 224808
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 224808
	COM "COM" (double, distance), size is 224808
	g1 "g1" (double, torsion(gamma)), size is 224808
	d1 "d1" (double, torsion(delta)), size is 224808
	e1 "e1" (double, torsion(epsilon)), size is 224808
	z1 "z1" (double, torsion(zeta)), size is 224808
	c1 "c1" (double, torsion(chin)), size is 224808
	a2 "a2" (double, torsion(alpha)), size is 224808
	b2 "b2" (double, torsion(beta)), size is 224808
	g2 "g2" (double, torsion(gamma)), size is 224808
	d2 "d2" (double, torsion(delta)), size is 224808
	c2 "c2" (double, torsion(chin)), size is 224808
	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 (16 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_g1-hist.dat (Standard Data File):  gamma_1
  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_a2-hist.dat (Standard Data File):  alpha_2
  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               : 0.0003 s (  0.09%)
TIME:		Trajectory Process : 0.3035 s ( 80.57%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0421 s ( 11.18%)
TIME:		Data File Write    : 0.0307 s (  8.16%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.3766 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2.1966 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.