CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 11:36:11
| Available memory: 1.772 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.c2]
	Reading '../ctraj.c2' 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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
    DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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@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, 63 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 83496 of 83496)
  Coordinate processing will occur on 83496 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*](39)
	Reference mask: [:1,2&!@H*](39)
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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
	:2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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@N9 :2@C4 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c2 (1-83496, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 83496 frames and processed 83496 frames.
TIME: Avg. throughput= 174658.4584 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 83496
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 83496
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 83496
	COM "COM" (double, distance), size is 83496
	g1 "g1" (double, torsion(gamma)), size is 83496
	d1 "d1" (double, torsion(delta)), size is 83496
	e1 "e1" (double, torsion(epsilon)), size is 83496
	z1 "z1" (double, torsion(zeta)), size is 83496
	c1 "c1" (double, torsion(chin)), size is 83496
	a2 "a2" (double, torsion(alpha)), size is 83496
	b2 "b2" (double, torsion(beta)), size is 83496
	g2 "g2" (double, torsion(gamma)), size is 83496
	d2 "d2" (double, torsion(delta)), size is 83496
	c2 "c2" (double, torsion(chin)), size is 83496

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.4781 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 0.4782 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, 63 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 83496 of 83496)
  Coordinate processing will occur on 83496 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c2 (1-83496, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 83496 frames and processed 83496 frames.
TIME: Avg. throughput= 1023323.0792 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: 83496 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 83496
  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: 83496 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 157 Coordinates out of bounds (-1)
	Warning: Frame 871 Coordinates out of bounds (-1)
	Warning: Frame 2480 Coordinates out of bounds (-1)
	Warning: Frame 5969 Coordinates out of bounds (-1)
	Warning: Frame 6152 Coordinates out of bounds (-1)
	Warning: Frame 10184 Coordinates out of bounds (-1)
	Warning: Frame 10239 Coordinates out of bounds (-1)
	Warning: Frame 11221 Coordinates out of bounds (-1)
	Warning: Frame 11830 Coordinates out of bounds (-1)
	Warning: Frame 16261 Coordinates out of bounds (-1)
	Warning: Frame 21639 Coordinates out of bounds (-1)
	Warning: Frame 21848 Coordinates out of bounds (-1)
	Warning: Frame 21849 Coordinates out of bounds (-1)
	Warning: Frame 23819 Coordinates out of bounds (-1)
	Warning: Frame 24686 Coordinates out of bounds (-1)
	Warning: Frame 25189 Coordinates out of bounds (-1)
	Warning: Frame 25190 Coordinates out of bounds (-1)
	Warning: Frame 25403 Coordinates out of bounds (-1)
	Warning: Frame 25496 Coordinates out of bounds (-1)
	Warning: Frame 27457 Coordinates out of bounds (-1)
	Warning: Frame 27550 Coordinates out of bounds (-1)
	Warning: Frame 28733 Coordinates out of bounds (-1)
	Warning: Frame 29868 Coordinates out of bounds (-1)
	Warning: Frame 33044 Coordinates out of bounds (-1)
	Warning: Frame 33634 Coordinates out of bounds (-1)
	Warning: Frame 33860 Coordinates out of bounds (-1)
	Warning: Frame 36262 Coordinates out of bounds (-1)
	Warning: Frame 36760 Coordinates out of bounds (-1)
	Warning: Frame 36871 Coordinates out of bounds (-1)
	Warning: Frame 36929 Coordinates out of bounds (-1)
	Warning: Frame 36984 Coordinates out of bounds (-1)
	Warning: Frame 37230 Coordinates out of bounds (-1)
	Warning: Frame 37330 Coordinates out of bounds (-1)
	Warning: Frame 37334 Coordinates out of bounds (-1)
	Warning: Frame 37335 Coordinates out of bounds (-1)
	Warning: Frame 37431 Coordinates out of bounds (-1)
	Warning: Frame 37950 Coordinates out of bounds (-1)
	Warning: Frame 38018 Coordinates out of bounds (-1)
	Warning: Frame 38176 Coordinates out of bounds (-1)
	Warning: Frame 38219 Coordinates out of bounds (-1)
	Warning: Frame 38403 Coordinates out of bounds (-1)
	Warning: Frame 38662 Coordinates out of bounds (-1)
	Warning: Frame 38674 Coordinates out of bounds (-1)
	Warning: Frame 39072 Coordinates out of bounds (-1)
	Warning: Frame 39087 Coordinates out of bounds (-1)
	Warning: Frame 39480 Coordinates out of bounds (-1)
	Warning: Frame 39925 Coordinates out of bounds (-1)
	Warning: Frame 40668 Coordinates out of bounds (-1)
	Warning: Frame 40820 Coordinates out of bounds (-1)
	Warning: Frame 41443 Coordinates out of bounds (-1)
	Warning: Frame 41616 Coordinates out of bounds (-1)
	Warning: Frame 42478 Coordinates out of bounds (-1)
	Warning: Frame 42919 Coordinates out of bounds (-1)
	Warning: Frame 43075 Coordinates out of bounds (-1)
	Warning: Frame 43348 Coordinates out of bounds (-1)
	Warning: Frame 43699 Coordinates out of bounds (-1)
	Warning: Frame 44015 Coordinates out of bounds (-1)
	Warning: Frame 44017 Coordinates out of bounds (-1)
	Warning: Frame 44053 Coordinates out of bounds (-1)
	Warning: Frame 44063 Coordinates out of bounds (-1)
	Warning: Frame 44239 Coordinates out of bounds (-1)
	Warning: Frame 44461 Coordinates out of bounds (-1)
	Warning: Frame 44681 Coordinates out of bounds (-1)
	Warning: Frame 44692 Coordinates out of bounds (-1)
	Warning: Frame 44713 Coordinates out of bounds (-1)
	Warning: Frame 44733 Coordinates out of bounds (-1)
	Warning: Frame 44865 Coordinates out of bounds (-1)
	Warning: Frame 44869 Coordinates out of bounds (-1)
	Warning: Frame 44879 Coordinates out of bounds (-1)
	Warning: Frame 44907 Coordinates out of bounds (-1)
	Warning: Frame 44913 Coordinates out of bounds (-1)
	Warning: Frame 44942 Coordinates out of bounds (-1)
	Warning: Frame 45138 Coordinates out of bounds (-1)
	Warning: Frame 45182 Coordinates out of bounds (-1)
	Warning: Frame 45313 Coordinates out of bounds (-1)
	Warning: Frame 45314 Coordinates out of bounds (-1)
	Warning: Frame 45315 Coordinates out of bounds (-1)
	Warning: Frame 45371 Coordinates out of bounds (-1)
	Warning: Frame 45395 Coordinates out of bounds (-1)
	Warning: Frame 45490 Coordinates out of bounds (-1)
	Warning: Frame 46958 Coordinates out of bounds (-1)
	Warning: Frame 49474 Coordinates out of bounds (-1)
	Warning: Frame 49480 Coordinates out of bounds (-1)
	Warning: Frame 49845 Coordinates out of bounds (-1)
	Warning: Frame 50612 Coordinates out of bounds (-1)
	Warning: Frame 51800 Coordinates out of bounds (-1)
	Warning: Frame 52017 Coordinates out of bounds (-1)
	Warning: Frame 52829 Coordinates out of bounds (-1)
	Warning: Frame 52954 Coordinates out of bounds (-1)
	Warning: Frame 55443 Coordinates out of bounds (-1)
	Warning: Frame 56994 Coordinates out of bounds (-1)
	Warning: Frame 59021 Coordinates out of bounds (-1)
	Warning: Frame 62084 Coordinates out of bounds (-1)
	Warning: Frame 62085 Coordinates out of bounds (-1)
	Warning: Frame 64866 Coordinates out of bounds (-1)
	Warning: Frame 67011 Coordinates out of bounds (-1)
	Warning: Frame 68169 Coordinates out of bounds (-1)
	Warning: Frame 70090 Coordinates out of bounds (-1)
	Warning: Frame 70340 Coordinates out of bounds (-1)
	Warning: Frame 70346 Coordinates out of bounds (-1)
	Warning: Frame 70480 Coordinates out of bounds (-1)
	Warning: Frame 70481 Coordinates out of bounds (-1)
	Warning: Frame 70842 Coordinates out of bounds (-1)
	Warning: Frame 70953 Coordinates out of bounds (-1)
	Warning: Frame 71097 Coordinates out of bounds (-1)
	Warning: Frame 71352 Coordinates out of bounds (-1)
	Warning: Frame 72157 Coordinates out of bounds (-1)
	Warning: Frame 72463 Coordinates out of bounds (-1)
	Warning: Frame 73223 Coordinates out of bounds (-1)
	Warning: Frame 78482 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 83386
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496
  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: 83496 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 83496

TIME: Analyses took 0.0142 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 83496
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 83496
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 83496
	COM "COM" (double, distance), size is 83496
	g1 "g1" (double, torsion(gamma)), size is 83496
	d1 "d1" (double, torsion(delta)), size is 83496
	e1 "e1" (double, torsion(epsilon)), size is 83496
	z1 "z1" (double, torsion(zeta)), size is 83496
	c1 "c1" (double, torsion(chin)), size is 83496
	a2 "a2" (double, torsion(alpha)), size is 83496
	b2 "b2" (double, torsion(beta)), size is 83496
	g2 "g2" (double, torsion(gamma)), size is 83496
	d2 "d2" (double, torsion(delta)), size is 83496
	c2 "c2" (double, torsion(chin)), size is 83496
	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 (  0.04%)
TIME:		Trajectory Process : 0.0816 s ( 48.40%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0142 s (  8.40%)
TIME:		Data File Write    : 0.0727 s ( 43.14%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.1686 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.6603 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.