CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 14:44:36
| Available memory: 1.588 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.c3]
	Reading '../ctraj.c3' 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    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,N2,H21,H22,N7,C8,H8,N9,O6, 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 chin]
    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 chin]
    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, 66 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 57870 of 57870)
  Coordinate processing will occur on 57870 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*](42)
	Reference mask: [:1,2&!@H*](42)
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,N2,H21,H22,N7,C8,H8,N9,O6]
	: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,N2,H21,H22,N7,C8,H8,N9,O6 (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 chin]
	 [: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 chin]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c3 (1-57870, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 57870 frames and processed 57870 frames.
TIME: Avg. throughput= 170310.5733 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 57870
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 57870
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 57870
	COM "COM" (double, distance), size is 57870
	g1 "g1" (double, torsion(gamma)), size is 57870
	d1 "d1" (double, torsion(delta)), size is 57870
	e1 "e1" (double, torsion(epsilon)), size is 57870
	z1 "z1" (double, torsion(zeta)), size is 57870
	c1 "c1" (double, torsion(chin)), size is 57870
	a2 "a2" (double, torsion(alpha)), size is 57870
	b2 "b2" (double, torsion(beta)), size is 57870
	g2 "g2" (double, torsion(gamma)), size is 57870
	d2 "d2" (double, torsion(delta)), size is 57870
	c2 "c2" (double, torsion(chin)), size is 57870

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.02%)
TIME:		Trajectory Process : 0.3398 s ( 99.96%)
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 0.3399 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, 66 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 57870 of 57870)
  Coordinate processing will occur on 57870 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c3 (1-57870, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 57870 frames and processed 57870 frames.
TIME: Avg. throughput= 678468.8434 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: 57870 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 57870
  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: 57870 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 78 Coordinates out of bounds (-1)
	Warning: Frame 963 Coordinates out of bounds (-1)
	Warning: Frame 2177 Coordinates out of bounds (-1)
	Warning: Frame 3741 Coordinates out of bounds (-1)
	Warning: Frame 3855 Coordinates out of bounds (-1)
	Warning: Frame 4240 Coordinates out of bounds (-1)
	Warning: Frame 4480 Coordinates out of bounds (-1)
	Warning: Frame 4697 Coordinates out of bounds (-1)
	Warning: Frame 4797 Coordinates out of bounds (-1)
	Warning: Frame 5459 Coordinates out of bounds (-1)
	Warning: Frame 5897 Coordinates out of bounds (-1)
	Warning: Frame 5918 Coordinates out of bounds (-1)
	Warning: Frame 6346 Coordinates out of bounds (-1)
	Warning: Frame 6748 Coordinates out of bounds (-1)
	Warning: Frame 6957 Coordinates out of bounds (-1)
	Warning: Frame 7608 Coordinates out of bounds (-1)
	Warning: Frame 7823 Coordinates out of bounds (-1)
	Warning: Frame 7969 Coordinates out of bounds (-1)
	Warning: Frame 8381 Coordinates out of bounds (-1)
	Warning: Frame 8382 Coordinates out of bounds (-1)
	Warning: Frame 8705 Coordinates out of bounds (-1)
	Warning: Frame 9635 Coordinates out of bounds (-1)
	Warning: Frame 9822 Coordinates out of bounds (-1)
	Warning: Frame 9896 Coordinates out of bounds (-1)
	Warning: Frame 10624 Coordinates out of bounds (-1)
	Warning: Frame 11550 Coordinates out of bounds (-1)
	Warning: Frame 11619 Coordinates out of bounds (-1)
	Warning: Frame 13006 Coordinates out of bounds (-1)
	Warning: Frame 13150 Coordinates out of bounds (-1)
	Warning: Frame 14223 Coordinates out of bounds (-1)
	Warning: Frame 15669 Coordinates out of bounds (-1)
	Warning: Frame 15670 Coordinates out of bounds (-1)
	Warning: Frame 15831 Coordinates out of bounds (-1)
	Warning: Frame 15832 Coordinates out of bounds (-1)
	Warning: Frame 16004 Coordinates out of bounds (-1)
	Warning: Frame 16023 Coordinates out of bounds (-1)
	Warning: Frame 16064 Coordinates out of bounds (-1)
	Warning: Frame 17073 Coordinates out of bounds (-1)
	Warning: Frame 17599 Coordinates out of bounds (-1)
	Warning: Frame 17981 Coordinates out of bounds (-1)
	Warning: Frame 18812 Coordinates out of bounds (-1)
	Warning: Frame 18879 Coordinates out of bounds (-1)
	Warning: Frame 18982 Coordinates out of bounds (-1)
	Warning: Frame 19946 Coordinates out of bounds (-1)
	Warning: Frame 20208 Coordinates out of bounds (-1)
	Warning: Frame 21197 Coordinates out of bounds (-1)
	Warning: Frame 21497 Coordinates out of bounds (-1)
	Warning: Frame 22226 Coordinates out of bounds (-1)
	Warning: Frame 22473 Coordinates out of bounds (-1)
	Warning: Frame 23006 Coordinates out of bounds (-1)
	Warning: Frame 24698 Coordinates out of bounds (-1)
	Warning: Frame 24968 Coordinates out of bounds (-1)
	Warning: Frame 25129 Coordinates out of bounds (-1)
	Warning: Frame 26616 Coordinates out of bounds (-1)
	Warning: Frame 26658 Coordinates out of bounds (-1)
	Warning: Frame 27732 Coordinates out of bounds (-1)
	Warning: Frame 28261 Coordinates out of bounds (-1)
	Warning: Frame 28262 Coordinates out of bounds (-1)
	Warning: Frame 28263 Coordinates out of bounds (-1)
	Warning: Frame 28911 Coordinates out of bounds (-1)
	Warning: Frame 29308 Coordinates out of bounds (-1)
	Warning: Frame 29309 Coordinates out of bounds (-1)
	Warning: Frame 29316 Coordinates out of bounds (-1)
	Warning: Frame 30609 Coordinates out of bounds (-1)
	Warning: Frame 31012 Coordinates out of bounds (-1)
	Warning: Frame 31013 Coordinates out of bounds (-1)
	Warning: Frame 31308 Coordinates out of bounds (-1)
	Warning: Frame 32266 Coordinates out of bounds (-1)
	Warning: Frame 32978 Coordinates out of bounds (-1)
	Warning: Frame 32979 Coordinates out of bounds (-1)
	Warning: Frame 33240 Coordinates out of bounds (-1)
	Warning: Frame 33636 Coordinates out of bounds (-1)
	Warning: Frame 33879 Coordinates out of bounds (-1)
	Warning: Frame 36055 Coordinates out of bounds (-1)
	Warning: Frame 36357 Coordinates out of bounds (-1)
	Warning: Frame 36499 Coordinates out of bounds (-1)
	Warning: Frame 37211 Coordinates out of bounds (-1)
	Warning: Frame 37215 Coordinates out of bounds (-1)
	Warning: Frame 37392 Coordinates out of bounds (-1)
	Warning: Frame 38326 Coordinates out of bounds (-1)
	Warning: Frame 38440 Coordinates out of bounds (-1)
	Warning: Frame 39072 Coordinates out of bounds (-1)
	Warning: Frame 39252 Coordinates out of bounds (-1)
	Warning: Frame 39636 Coordinates out of bounds (-1)
	Warning: Frame 40429 Coordinates out of bounds (-1)
	Warning: Frame 40928 Coordinates out of bounds (-1)
	Warning: Frame 41002 Coordinates out of bounds (-1)
	Warning: Frame 41723 Coordinates out of bounds (-1)
	Warning: Frame 41724 Coordinates out of bounds (-1)
	Warning: Frame 41726 Coordinates out of bounds (-1)
	Warning: Frame 42193 Coordinates out of bounds (-1)
	Warning: Frame 43140 Coordinates out of bounds (-1)
	Warning: Frame 43141 Coordinates out of bounds (-1)
	Warning: Frame 43142 Coordinates out of bounds (-1)
	Warning: Frame 43143 Coordinates out of bounds (-1)
	Warning: Frame 43149 Coordinates out of bounds (-1)
	Warning: Frame 45133 Coordinates out of bounds (-1)
	Warning: Frame 45136 Coordinates out of bounds (-1)
	Warning: Frame 45205 Coordinates out of bounds (-1)
	Warning: Frame 45206 Coordinates out of bounds (-1)
	Warning: Frame 45402 Coordinates out of bounds (-1)
	Warning: Frame 47075 Coordinates out of bounds (-1)
	Warning: Frame 47185 Coordinates out of bounds (-1)
	Warning: Frame 47186 Coordinates out of bounds (-1)
	Warning: Frame 47365 Coordinates out of bounds (-1)
	Warning: Frame 47929 Coordinates out of bounds (-1)
	Warning: Frame 48831 Coordinates out of bounds (-1)
	Warning: Frame 48834 Coordinates out of bounds (-1)
	Warning: Frame 50126 Coordinates out of bounds (-1)
	Warning: Frame 50756 Coordinates out of bounds (-1)
	Warning: Frame 51711 Coordinates out of bounds (-1)
	Warning: Frame 52292 Coordinates out of bounds (-1)
	Warning: Frame 52655 Coordinates out of bounds (-1)
	Warning: Frame 52955 Coordinates out of bounds (-1)
	Warning: Frame 54397 Coordinates out of bounds (-1)
	Warning: Frame 54708 Coordinates out of bounds (-1)
	Warning: Frame 55833 Coordinates out of bounds (-1)
	Warning: Frame 56127 Coordinates out of bounds (-1)
	Warning: Frame 56641 Coordinates out of bounds (-1)
	Warning: Frame 56642 Coordinates out of bounds (-1)
	Warning: Frame 56769 Coordinates out of bounds (-1)
	Warning: Frame 56770 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 57748
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870
  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: 57870 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 57870

TIME: Analyses took 0.0128 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 57870
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 57870
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 57870
	COM "COM" (double, distance), size is 57870
	g1 "g1" (double, torsion(gamma)), size is 57870
	d1 "d1" (double, torsion(delta)), size is 57870
	e1 "e1" (double, torsion(epsilon)), size is 57870
	z1 "z1" (double, torsion(zeta)), size is 57870
	c1 "c1" (double, torsion(chin)), size is 57870
	a2 "a2" (double, torsion(alpha)), size is 57870
	b2 "b2" (double, torsion(beta)), size is 57870
	g2 "g2" (double, torsion(gamma)), size is 57870
	d2 "d2" (double, torsion(delta)), size is 57870
	c2 "c2" (double, torsion(chin)), size is 57870
	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               : 0.0001 s (  0.08%)
TIME:		Trajectory Process : 0.0853 s ( 71.84%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0128 s ( 10.79%)
TIME:		Data File Write    : 0.0205 s ( 17.26%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.1187 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.4716 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.