CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 18:13:36
| Available memory: 3.766 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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@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@N9 :1@C4 type chi]
    DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4]
              Output range is -180 to 180 degrees.
  [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
    DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5']
              Output range is -180 to 180 degrees.
  [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
    DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4']
              Output range is -180 to 180 degrees.
  [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
    DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3']
              Output range is -180 to 180 degrees.
  [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
    DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3']
              Output range is -180 to 180 degrees.
  [dihedral c2 :2@O4' :2@C1' :2@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, 64 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 17259 of 17259)
  Coordinate processing will occur on 17259 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*](40)
	Reference mask: [:1,2&!@H*](40)
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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@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@N9 :1@C4 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1)
  9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
	 [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
  10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
	 [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1)
  11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
	 [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1)
  12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
	 [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1)
  13: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c2 (1-17259, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 17259 frames and processed 17259 frames.
TIME: Avg. throughput= 80653.6785 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 17259
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 17259
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 17259
	COM "COM" (double, distance), size is 17259
	g1 "g1" (double, torsion(gamma)), size is 17259
	d1 "d1" (double, torsion(delta)), size is 17259
	e1 "e1" (double, torsion(epsilon)), size is 17259
	z1 "z1" (double, torsion(zeta)), size is 17259
	c1 "c1" (double, torsion(chin)), size is 17259
	a2 "a2" (double, torsion(alpha)), size is 17259
	b2 "b2" (double, torsion(beta)), size is 17259
	g2 "g2" (double, torsion(gamma)), size is 17259
	d2 "d2" (double, torsion(delta)), size is 17259
	c2 "c2" (double, torsion(chin)), size is 17259

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.2140 s ( 99.95%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.02%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2141 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, 64 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 17259 of 17259)
  Coordinate processing will occur on 17259 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 (1-17259, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 17259 frames and processed 17259 frames.
TIME: Avg. throughput= 149062.0466 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: 17259 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 17259
  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: 17259 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 260 Coordinates out of bounds (-1)
	Warning: Frame 264 Coordinates out of bounds (-1)
	Warning: Frame 460 Coordinates out of bounds (-1)
	Warning: Frame 463 Coordinates out of bounds (-1)
	Warning: Frame 1312 Coordinates out of bounds (-1)
	Warning: Frame 2592 Coordinates out of bounds (-1)
	Warning: Frame 2593 Coordinates out of bounds (-1)
	Warning: Frame 2606 Coordinates out of bounds (-1)
	Warning: Frame 2607 Coordinates out of bounds (-1)
	Warning: Frame 2608 Coordinates out of bounds (-1)
	Warning: Frame 2609 Coordinates out of bounds (-1)
	Warning: Frame 2610 Coordinates out of bounds (-1)
	Warning: Frame 2611 Coordinates out of bounds (-1)
	Warning: Frame 2756 Coordinates out of bounds (-1)
	Warning: Frame 2791 Coordinates out of bounds (-1)
	Warning: Frame 2884 Coordinates out of bounds (-1)
	Warning: Frame 2885 Coordinates out of bounds (-1)
	Warning: Frame 2886 Coordinates out of bounds (-1)
	Warning: Frame 2887 Coordinates out of bounds (-1)
	Warning: Frame 3017 Coordinates out of bounds (-1)
	Warning: Frame 3214 Coordinates out of bounds (-1)
	Warning: Frame 3320 Coordinates out of bounds (-1)
	Warning: Frame 3321 Coordinates out of bounds (-1)
	Warning: Frame 4195 Coordinates out of bounds (-1)
	Warning: Frame 4196 Coordinates out of bounds (-1)
	Warning: Frame 4275 Coordinates out of bounds (-1)
	Warning: Frame 4383 Coordinates out of bounds (-1)
	Warning: Frame 4525 Coordinates out of bounds (-1)
	Warning: Frame 4550 Coordinates out of bounds (-1)
	Warning: Frame 4620 Coordinates out of bounds (-1)
	Warning: Frame 4790 Coordinates out of bounds (-1)
	Warning: Frame 4923 Coordinates out of bounds (-1)
	Warning: Frame 5239 Coordinates out of bounds (-1)
	Warning: Frame 5565 Coordinates out of bounds (-1)
	Warning: Frame 5850 Coordinates out of bounds (-1)
	Warning: Frame 5851 Coordinates out of bounds (-1)
	Warning: Frame 6152 Coordinates out of bounds (-1)
	Warning: Frame 6219 Coordinates out of bounds (-1)
	Warning: Frame 6245 Coordinates out of bounds (-1)
	Warning: Frame 6253 Coordinates out of bounds (-1)
	Warning: Frame 6282 Coordinates out of bounds (-1)
	Warning: Frame 6421 Coordinates out of bounds (-1)
	Warning: Frame 6422 Coordinates out of bounds (-1)
	Warning: Frame 6618 Coordinates out of bounds (-1)
	Warning: Frame 7459 Coordinates out of bounds (-1)
	Warning: Frame 7602 Coordinates out of bounds (-1)
	Warning: Frame 7896 Coordinates out of bounds (-1)
	Warning: Frame 8243 Coordinates out of bounds (-1)
	Warning: Frame 8598 Coordinates out of bounds (-1)
	Warning: Frame 8813 Coordinates out of bounds (-1)
	Warning: Frame 8893 Coordinates out of bounds (-1)
	Warning: Frame 8941 Coordinates out of bounds (-1)
	Warning: Frame 9131 Coordinates out of bounds (-1)
	Warning: Frame 9496 Coordinates out of bounds (-1)
	Warning: Frame 9498 Coordinates out of bounds (-1)
	Warning: Frame 10471 Coordinates out of bounds (-1)
	Warning: Frame 10600 Coordinates out of bounds (-1)
	Warning: Frame 11378 Coordinates out of bounds (-1)
	Warning: Frame 11760 Coordinates out of bounds (-1)
	Warning: Frame 11781 Coordinates out of bounds (-1)
	Warning: Frame 11942 Coordinates out of bounds (-1)
	Warning: Frame 12283 Coordinates out of bounds (-1)
	Warning: Frame 12795 Coordinates out of bounds (-1)
	Warning: Frame 12907 Coordinates out of bounds (-1)
	Warning: Frame 12908 Coordinates out of bounds (-1)
	Warning: Frame 13182 Coordinates out of bounds (-1)
	Warning: Frame 13345 Coordinates out of bounds (-1)
	Warning: Frame 13489 Coordinates out of bounds (-1)
	Warning: Frame 13490 Coordinates out of bounds (-1)
	Warning: Frame 13546 Coordinates out of bounds (-1)
	Warning: Frame 14057 Coordinates out of bounds (-1)
	Warning: Frame 14338 Coordinates out of bounds (-1)
	Warning: Frame 14629 Coordinates out of bounds (-1)
	Warning: Frame 14730 Coordinates out of bounds (-1)
	Warning: Frame 14908 Coordinates out of bounds (-1)
	Warning: Frame 14925 Coordinates out of bounds (-1)
	Warning: Frame 15055 Coordinates out of bounds (-1)
	Warning: Frame 15231 Coordinates out of bounds (-1)
	Warning: Frame 15411 Coordinates out of bounds (-1)
	Warning: Frame 16194 Coordinates out of bounds (-1)
	Warning: Frame 16383 Coordinates out of bounds (-1)
	Warning: Frame 16535 Coordinates out of bounds (-1)
	Warning: Frame 16679 Coordinates out of bounds (-1)
	Warning: Frame 16795 Coordinates out of bounds (-1)
	Warning: Frame 16858 Coordinates out of bounds (-1)
	Warning: Frame 16950 Coordinates out of bounds (-1)
	Warning: Frame 17210 Coordinates out of bounds (-1)
	Warning: Frame 17212 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 17171
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259
  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: 17259 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 17259

TIME: Analyses took 0.0058 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 17259
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 17259
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 17259
	COM "COM" (double, distance), size is 17259
	g1 "g1" (double, torsion(gamma)), size is 17259
	d1 "d1" (double, torsion(delta)), size is 17259
	e1 "e1" (double, torsion(epsilon)), size is 17259
	z1 "z1" (double, torsion(zeta)), size is 17259
	c1 "c1" (double, torsion(chin)), size is 17259
	a2 "a2" (double, torsion(alpha)), size is 17259
	b2 "b2" (double, torsion(beta)), size is 17259
	g2 "g2" (double, torsion(gamma)), size is 17259
	d2 "d2" (double, torsion(delta)), size is 17259
	c2 "c2" (double, torsion(chin)), size is 17259
	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 (  0.00%)
TIME:		Trajectory Process : 0.1158 s ( 10.04%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0058 s (  0.50%)
TIME:		Data File Write    : 1.0311 s ( 89.45%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.1527 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2.1159 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.