CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 12:06:57
| Available memory: 1.224 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.c4]
	Reading '../ctraj.c4' 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@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, 60 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5397 of 5397)
  Coordinate processing will occur on 5397 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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@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.c4 (1-5397, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 5397 frames and processed 5397 frames.
TIME: Avg. throughput= 112580.5711 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 5397
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 5397
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 5397
	COM "COM" (double, distance), size is 5397
	g1 "g1" (double, torsion(gamma)), size is 5397
	d1 "d1" (double, torsion(delta)), size is 5397
	e1 "e1" (double, torsion(epsilon)), size is 5397
	z1 "z1" (double, torsion(zeta)), size is 5397
	c1 "c1" (double, torsion(chin)), size is 5397
	a2 "a2" (double, torsion(alpha)), size is 5397
	b2 "b2" (double, torsion(beta)), size is 5397
	g2 "g2" (double, torsion(gamma)), size is 5397
	d2 "d2" (double, torsion(delta)), size is 5397
	c2 "c2" (double, torsion(chin)), size is 5397

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.11%)
TIME:		Trajectory Process : 0.0479 s ( 99.73%)
TIME:		Action Post        : 0.0000 s (  0.01%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.08%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0481 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, 60 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5397 of 5397)
  Coordinate processing will occur on 5397 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c4 (1-5397, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 5397 frames and processed 5397 frames.
TIME: Avg. throughput= 482176.3602 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: 5397 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 5397
  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: 5397 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 1 Coordinates out of bounds (-1)
	Warning: Frame 17 Coordinates out of bounds (-1)
	Warning: Frame 19 Coordinates out of bounds (-1)
	Warning: Frame 27 Coordinates out of bounds (-1)
	Warning: Frame 44 Coordinates out of bounds (-1)
	Warning: Frame 104 Coordinates out of bounds (-1)
	Warning: Frame 105 Coordinates out of bounds (-1)
	Warning: Frame 106 Coordinates out of bounds (-1)
	Warning: Frame 118 Coordinates out of bounds (-1)
	Warning: Frame 141 Coordinates out of bounds (-1)
	Warning: Frame 142 Coordinates out of bounds (-1)
	Warning: Frame 144 Coordinates out of bounds (-1)
	Warning: Frame 145 Coordinates out of bounds (-1)
	Warning: Frame 146 Coordinates out of bounds (-1)
	Warning: Frame 147 Coordinates out of bounds (-1)
	Warning: Frame 157 Coordinates out of bounds (-1)
	Warning: Frame 180 Coordinates out of bounds (-1)
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	Warning: Frame 4941 Coordinates out of bounds (-1)
	Warning: Frame 4947 Coordinates out of bounds (-1)
	Warning: Frame 4963 Coordinates out of bounds (-1)
	Warning: Frame 4964 Coordinates out of bounds (-1)
	Warning: Frame 4978 Coordinates out of bounds (-1)
	Warning: Frame 4979 Coordinates out of bounds (-1)
	Warning: Frame 4980 Coordinates out of bounds (-1)
	Warning: Frame 4987 Coordinates out of bounds (-1)
	Warning: Frame 4995 Coordinates out of bounds (-1)
	Warning: Frame 4996 Coordinates out of bounds (-1)
	Warning: Frame 5047 Coordinates out of bounds (-1)
	Warning: Frame 5051 Coordinates out of bounds (-1)
	Warning: Frame 5054 Coordinates out of bounds (-1)
	Warning: Frame 5060 Coordinates out of bounds (-1)
	Warning: Frame 5062 Coordinates out of bounds (-1)
	Warning: Frame 5063 Coordinates out of bounds (-1)
	Warning: Frame 5064 Coordinates out of bounds (-1)
	Warning: Frame 5066 Coordinates out of bounds (-1)
	Warning: Frame 5067 Coordinates out of bounds (-1)
	Warning: Frame 5075 Coordinates out of bounds (-1)
	Warning: Frame 5094 Coordinates out of bounds (-1)
	Warning: Frame 5095 Coordinates out of bounds (-1)
	Warning: Frame 5096 Coordinates out of bounds (-1)
	Warning: Frame 5099 Coordinates out of bounds (-1)
	Warning: Frame 5119 Coordinates out of bounds (-1)
	Warning: Frame 5143 Coordinates out of bounds (-1)
	Warning: Frame 5144 Coordinates out of bounds (-1)
	Warning: Frame 5145 Coordinates out of bounds (-1)
	Warning: Frame 5146 Coordinates out of bounds (-1)
	Warning: Frame 5147 Coordinates out of bounds (-1)
	Warning: Frame 5159 Coordinates out of bounds (-1)
	Warning: Frame 5165 Coordinates out of bounds (-1)
	Warning: Frame 5169 Coordinates out of bounds (-1)
	Warning: Frame 5183 Coordinates out of bounds (-1)
	Warning: Frame 5195 Coordinates out of bounds (-1)
	Warning: Frame 5199 Coordinates out of bounds (-1)
	Warning: Frame 5200 Coordinates out of bounds (-1)
	Warning: Frame 5201 Coordinates out of bounds (-1)
	Warning: Frame 5202 Coordinates out of bounds (-1)
	Warning: Frame 5205 Coordinates out of bounds (-1)
	Warning: Frame 5218 Coordinates out of bounds (-1)
	Warning: Frame 5220 Coordinates out of bounds (-1)
	Warning: Frame 5221 Coordinates out of bounds (-1)
	Warning: Frame 5225 Coordinates out of bounds (-1)
	Warning: Frame 5226 Coordinates out of bounds (-1)
	Warning: Frame 5231 Coordinates out of bounds (-1)
	Warning: Frame 5232 Coordinates out of bounds (-1)
	Warning: Frame 5247 Coordinates out of bounds (-1)
	Warning: Frame 5248 Coordinates out of bounds (-1)
	Warning: Frame 5249 Coordinates out of bounds (-1)
	Warning: Frame 5252 Coordinates out of bounds (-1)
	Warning: Frame 5253 Coordinates out of bounds (-1)
	Warning: Frame 5257 Coordinates out of bounds (-1)
	Warning: Frame 5264 Coordinates out of bounds (-1)
	Warning: Frame 5303 Coordinates out of bounds (-1)
	Warning: Frame 5304 Coordinates out of bounds (-1)
	Warning: Frame 5308 Coordinates out of bounds (-1)
	Warning: Frame 5310 Coordinates out of bounds (-1)
	Warning: Frame 5316 Coordinates out of bounds (-1)
	Warning: Frame 5317 Coordinates out of bounds (-1)
	Warning: Frame 5331 Coordinates out of bounds (-1)
	Warning: Frame 5332 Coordinates out of bounds (-1)
	Warning: Frame 5333 Coordinates out of bounds (-1)
	Warning: Frame 5353 Coordinates out of bounds (-1)
	Warning: Frame 5372 Coordinates out of bounds (-1)
	Warning: Frame 5373 Coordinates out of bounds (-1)
	Warning: Frame 5374 Coordinates out of bounds (-1)
	Warning: Frame 5388 Coordinates out of bounds (-1)
	Warning: Frame 5389 Coordinates out of bounds (-1)
	Warning: Frame 5390 Coordinates out of bounds (-1)
	Warning: Frame 5391 Coordinates out of bounds (-1)
	Warning: Frame 5392 Coordinates out of bounds (-1)
	Warning: Frame 5393 Coordinates out of bounds (-1)
	Warning: Frame 5395 Coordinates out of bounds (-1)
	Warning: Frame 5396 Coordinates out of bounds (-1)
	Warning: Frame 5397 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 4613
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397
  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: 5397 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 5397

TIME: Analyses took 0.0024 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 5397
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 5397
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 5397
	COM "COM" (double, distance), size is 5397
	g1 "g1" (double, torsion(gamma)), size is 5397
	d1 "d1" (double, torsion(delta)), size is 5397
	e1 "e1" (double, torsion(epsilon)), size is 5397
	z1 "z1" (double, torsion(zeta)), size is 5397
	c1 "c1" (double, torsion(chin)), size is 5397
	a2 "a2" (double, torsion(alpha)), size is 5397
	b2 "b2" (double, torsion(beta)), size is 5397
	g2 "g2" (double, torsion(gamma)), size is 5397
	d2 "d2" (double, torsion(delta)), size is 5397
	c2 "c2" (double, torsion(chin)), size is 5397
	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               : 0.0000 s (  0.06%)
TIME:		Trajectory Process : 0.0112 s ( 22.76%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0024 s (  4.90%)
TIME:		Data File Write    : 0.0355 s ( 72.23%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0492 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1113 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.