CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 17:04:11
| Available memory: 3.890 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.c1]
	Reading '../ctraj.c1' 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,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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@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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19588 of 19588)
  Coordinate processing will occur on 19588 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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 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@N9 :2@C4 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c1 (1-19588, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 19588 frames and processed 19588 frames.
TIME: Avg. throughput= 83637.2021 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 19588
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 19588
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 19588
	COM "COM" (double, distance), size is 19588
	g1 "g1" (double, torsion(gamma)), size is 19588
	d1 "d1" (double, torsion(delta)), size is 19588
	e1 "e1" (double, torsion(epsilon)), size is 19588
	z1 "z1" (double, torsion(zeta)), size is 19588
	c1 "c1" (double, torsion(chin)), size is 19588
	a2 "a2" (double, torsion(alpha)), size is 19588
	b2 "b2" (double, torsion(beta)), size is 19588
	g2 "g2" (double, torsion(gamma)), size is 19588
	d2 "d2" (double, torsion(delta)), size is 19588
	c2 "c2" (double, torsion(chin)), size is 19588

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.2342 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 0.2343 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19588 of 19588)
  Coordinate processing will occur on 19588 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c1 (1-19588, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 19588 frames and processed 19588 frames.
TIME: Avg. throughput= 412404.9940 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: 19588 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 19588
  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: 19588 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 381 Coordinates out of bounds (-1)
	Warning: Frame 918 Coordinates out of bounds (-1)
	Warning: Frame 919 Coordinates out of bounds (-1)
	Warning: Frame 1137 Coordinates out of bounds (-1)
	Warning: Frame 1184 Coordinates out of bounds (-1)
	Warning: Frame 1511 Coordinates out of bounds (-1)
	Warning: Frame 1530 Coordinates out of bounds (-1)
	Warning: Frame 1676 Coordinates out of bounds (-1)
	Warning: Frame 1777 Coordinates out of bounds (-1)
	Warning: Frame 1881 Coordinates out of bounds (-1)
	Warning: Frame 1973 Coordinates out of bounds (-1)
	Warning: Frame 1980 Coordinates out of bounds (-1)
	Warning: Frame 2027 Coordinates out of bounds (-1)
	Warning: Frame 2598 Coordinates out of bounds (-1)
	Warning: Frame 2699 Coordinates out of bounds (-1)
	Warning: Frame 2733 Coordinates out of bounds (-1)
	Warning: Frame 3084 Coordinates out of bounds (-1)
	Warning: Frame 3630 Coordinates out of bounds (-1)
	Warning: Frame 3681 Coordinates out of bounds (-1)
	Warning: Frame 3913 Coordinates out of bounds (-1)
	Warning: Frame 4393 Coordinates out of bounds (-1)
	Warning: Frame 4421 Coordinates out of bounds (-1)
	Warning: Frame 4422 Coordinates out of bounds (-1)
	Warning: Frame 4565 Coordinates out of bounds (-1)
	Warning: Frame 4684 Coordinates out of bounds (-1)
	Warning: Frame 4790 Coordinates out of bounds (-1)
	Warning: Frame 4791 Coordinates out of bounds (-1)
	Warning: Frame 5158 Coordinates out of bounds (-1)
	Warning: Frame 5754 Coordinates out of bounds (-1)
	Warning: Frame 6046 Coordinates out of bounds (-1)
	Warning: Frame 6192 Coordinates out of bounds (-1)
	Warning: Frame 6217 Coordinates out of bounds (-1)
	Warning: Frame 6462 Coordinates out of bounds (-1)
	Warning: Frame 6525 Coordinates out of bounds (-1)
	Warning: Frame 6533 Coordinates out of bounds (-1)
	Warning: Frame 6540 Coordinates out of bounds (-1)
	Warning: Frame 6547 Coordinates out of bounds (-1)
	Warning: Frame 6759 Coordinates out of bounds (-1)
	Warning: Frame 7162 Coordinates out of bounds (-1)
	Warning: Frame 7177 Coordinates out of bounds (-1)
	Warning: Frame 7321 Coordinates out of bounds (-1)
	Warning: Frame 7469 Coordinates out of bounds (-1)
	Warning: Frame 7772 Coordinates out of bounds (-1)
	Warning: Frame 7857 Coordinates out of bounds (-1)
	Warning: Frame 8069 Coordinates out of bounds (-1)
	Warning: Frame 8605 Coordinates out of bounds (-1)
	Warning: Frame 9019 Coordinates out of bounds (-1)
	Warning: Frame 10144 Coordinates out of bounds (-1)
	Warning: Frame 10145 Coordinates out of bounds (-1)
	Warning: Frame 10191 Coordinates out of bounds (-1)
	Warning: Frame 10208 Coordinates out of bounds (-1)
	Warning: Frame 10221 Coordinates out of bounds (-1)
	Warning: Frame 10441 Coordinates out of bounds (-1)
	Warning: Frame 10523 Coordinates out of bounds (-1)
	Warning: Frame 10596 Coordinates out of bounds (-1)
	Warning: Frame 10597 Coordinates out of bounds (-1)
	Warning: Frame 10762 Coordinates out of bounds (-1)
	Warning: Frame 10855 Coordinates out of bounds (-1)
	Warning: Frame 11642 Coordinates out of bounds (-1)
	Warning: Frame 11811 Coordinates out of bounds (-1)
	Warning: Frame 11812 Coordinates out of bounds (-1)
	Warning: Frame 11983 Coordinates out of bounds (-1)
	Warning: Frame 11993 Coordinates out of bounds (-1)
	Warning: Frame 11994 Coordinates out of bounds (-1)
	Warning: Frame 12019 Coordinates out of bounds (-1)
	Warning: Frame 12462 Coordinates out of bounds (-1)
	Warning: Frame 13484 Coordinates out of bounds (-1)
	Warning: Frame 13497 Coordinates out of bounds (-1)
	Warning: Frame 13505 Coordinates out of bounds (-1)
	Warning: Frame 14025 Coordinates out of bounds (-1)
	Warning: Frame 14231 Coordinates out of bounds (-1)
	Warning: Frame 14331 Coordinates out of bounds (-1)
	Warning: Frame 14403 Coordinates out of bounds (-1)
	Warning: Frame 14604 Coordinates out of bounds (-1)
	Warning: Frame 14706 Coordinates out of bounds (-1)
	Warning: Frame 14828 Coordinates out of bounds (-1)
	Warning: Frame 14884 Coordinates out of bounds (-1)
	Warning: Frame 14897 Coordinates out of bounds (-1)
	Warning: Frame 14920 Coordinates out of bounds (-1)
	Warning: Frame 14929 Coordinates out of bounds (-1)
	Warning: Frame 14943 Coordinates out of bounds (-1)
	Warning: Frame 14977 Coordinates out of bounds (-1)
	Warning: Frame 15079 Coordinates out of bounds (-1)
	Warning: Frame 15306 Coordinates out of bounds (-1)
	Warning: Frame 15412 Coordinates out of bounds (-1)
	Warning: Frame 15579 Coordinates out of bounds (-1)
	Warning: Frame 15593 Coordinates out of bounds (-1)
	Warning: Frame 15610 Coordinates out of bounds (-1)
	Warning: Frame 15866 Coordinates out of bounds (-1)
	Warning: Frame 16044 Coordinates out of bounds (-1)
	Warning: Frame 16046 Coordinates out of bounds (-1)
	Warning: Frame 16065 Coordinates out of bounds (-1)
	Warning: Frame 16082 Coordinates out of bounds (-1)
	Warning: Frame 16086 Coordinates out of bounds (-1)
	Warning: Frame 16406 Coordinates out of bounds (-1)
	Warning: Frame 16904 Coordinates out of bounds (-1)
	Warning: Frame 16905 Coordinates out of bounds (-1)
	Warning: Frame 16924 Coordinates out of bounds (-1)
	Warning: Frame 17166 Coordinates out of bounds (-1)
	Warning: Frame 17233 Coordinates out of bounds (-1)
	Warning: Frame 17329 Coordinates out of bounds (-1)
	Warning: Frame 17467 Coordinates out of bounds (-1)
	Warning: Frame 17626 Coordinates out of bounds (-1)
	Warning: Frame 17700 Coordinates out of bounds (-1)
	Warning: Frame 17716 Coordinates out of bounds (-1)
	Warning: Frame 17751 Coordinates out of bounds (-1)
	Warning: Frame 17925 Coordinates out of bounds (-1)
	Warning: Frame 18040 Coordinates out of bounds (-1)
	Warning: Frame 18105 Coordinates out of bounds (-1)
	Warning: Frame 18417 Coordinates out of bounds (-1)
	Warning: Frame 18482 Coordinates out of bounds (-1)
	Warning: Frame 18529 Coordinates out of bounds (-1)
	Warning: Frame 18530 Coordinates out of bounds (-1)
	Warning: Frame 18601 Coordinates out of bounds (-1)
	Warning: Frame 19086 Coordinates out of bounds (-1)
	Warning: Frame 19314 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 19472
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588
  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: 19588 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 19588

TIME: Analyses took 0.0069 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 19588
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 19588
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 19588
	COM "COM" (double, distance), size is 19588
	g1 "g1" (double, torsion(gamma)), size is 19588
	d1 "d1" (double, torsion(delta)), size is 19588
	e1 "e1" (double, torsion(epsilon)), size is 19588
	z1 "z1" (double, torsion(zeta)), size is 19588
	c1 "c1" (double, torsion(chin)), size is 19588
	a2 "a2" (double, torsion(alpha)), size is 19588
	b2 "b2" (double, torsion(beta)), size is 19588
	g2 "g2" (double, torsion(gamma)), size is 19588
	d2 "d2" (double, torsion(delta)), size is 19588
	c2 "c2" (double, torsion(chin)), size is 19588
	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 (  0.01%)
TIME:		Trajectory Process : 0.0475 s (  9.27%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0069 s (  1.34%)
TIME:		Data File Write    : 0.4580 s ( 89.38%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.5124 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.2270 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.