CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 10:33:16
| Available memory: 3.482 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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@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 4472 of 4472)
  Coordinate processing will occur on 4472 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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@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 (1-4472, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 4472 frames and processed 4472 frames.
TIME: Avg. throughput= 109621.2771 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 4472
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 4472
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 4472
	COM "COM" (double, distance), size is 4472
	g1 "g1" (double, torsion(gamma)), size is 4472
	d1 "d1" (double, torsion(delta)), size is 4472
	e1 "e1" (double, torsion(epsilon)), size is 4472
	z1 "z1" (double, torsion(zeta)), size is 4472
	c1 "c1" (double, torsion(chin)), size is 4472
	a2 "a2" (double, torsion(alpha)), size is 4472
	b2 "b2" (double, torsion(beta)), size is 4472
	g2 "g2" (double, torsion(gamma)), size is 4472
	d2 "d2" (double, torsion(delta)), size is 4472
	c2 "c2" (double, torsion(chin)), size is 4472

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.12%)
TIME:		Trajectory Process : 0.0408 s ( 99.72%)
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 0.0409 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 4472 of 4472)
  Coordinate processing will occur on 4472 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 (1-4472, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 4472 frames and processed 4472 frames.
TIME: Avg. throughput= 441722.6393 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: 4472 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 4472
  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: 4472 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 3 Coordinates out of bounds (-1)
	Warning: Frame 35 Coordinates out of bounds (-1)
	Warning: Frame 85 Coordinates out of bounds (-1)
	Warning: Frame 104 Coordinates out of bounds (-1)
	Warning: Frame 107 Coordinates out of bounds (-1)
	Warning: Frame 169 Coordinates out of bounds (-1)
	Warning: Frame 223 Coordinates out of bounds (-1)
	Warning: Frame 267 Coordinates out of bounds (-1)
	Warning: Frame 286 Coordinates out of bounds (-1)
	Warning: Frame 300 Coordinates out of bounds (-1)
	Warning: Frame 312 Coordinates out of bounds (-1)
	Warning: Frame 320 Coordinates out of bounds (-1)
	Warning: Frame 327 Coordinates out of bounds (-1)
	Warning: Frame 391 Coordinates out of bounds (-1)
	Warning: Frame 410 Coordinates out of bounds (-1)
	Warning: Frame 411 Coordinates out of bounds (-1)
	Warning: Frame 413 Coordinates out of bounds (-1)
	Warning: Frame 458 Coordinates out of bounds (-1)
	Warning: Frame 694 Coordinates out of bounds (-1)
	Warning: Frame 700 Coordinates out of bounds (-1)
	Warning: Frame 769 Coordinates out of bounds (-1)
	Warning: Frame 816 Coordinates out of bounds (-1)
	Warning: Frame 817 Coordinates out of bounds (-1)
	Warning: Frame 885 Coordinates out of bounds (-1)
	Warning: Frame 911 Coordinates out of bounds (-1)
	Warning: Frame 939 Coordinates out of bounds (-1)
	Warning: Frame 949 Coordinates out of bounds (-1)
	Warning: Frame 1009 Coordinates out of bounds (-1)
	Warning: Frame 1013 Coordinates out of bounds (-1)
	Warning: Frame 1028 Coordinates out of bounds (-1)
	Warning: Frame 1037 Coordinates out of bounds (-1)
	Warning: Frame 1103 Coordinates out of bounds (-1)
	Warning: Frame 1173 Coordinates out of bounds (-1)
	Warning: Frame 1223 Coordinates out of bounds (-1)
	Warning: Frame 1225 Coordinates out of bounds (-1)
	Warning: Frame 1227 Coordinates out of bounds (-1)
	Warning: Frame 1231 Coordinates out of bounds (-1)
	Warning: Frame 1263 Coordinates out of bounds (-1)
	Warning: Frame 1381 Coordinates out of bounds (-1)
	Warning: Frame 1540 Coordinates out of bounds (-1)
	Warning: Frame 1615 Coordinates out of bounds (-1)
	Warning: Frame 1619 Coordinates out of bounds (-1)
	Warning: Frame 1625 Coordinates out of bounds (-1)
	Warning: Frame 1699 Coordinates out of bounds (-1)
	Warning: Frame 1731 Coordinates out of bounds (-1)
	Warning: Frame 1750 Coordinates out of bounds (-1)
	Warning: Frame 1759 Coordinates out of bounds (-1)
	Warning: Frame 1789 Coordinates out of bounds (-1)
	Warning: Frame 1803 Coordinates out of bounds (-1)
	Warning: Frame 1830 Coordinates out of bounds (-1)
	Warning: Frame 1850 Coordinates out of bounds (-1)
	Warning: Frame 1866 Coordinates out of bounds (-1)
	Warning: Frame 1886 Coordinates out of bounds (-1)
	Warning: Frame 1909 Coordinates out of bounds (-1)
	Warning: Frame 1932 Coordinates out of bounds (-1)
	Warning: Frame 1933 Coordinates out of bounds (-1)
	Warning: Frame 1970 Coordinates out of bounds (-1)
	Warning: Frame 1971 Coordinates out of bounds (-1)
	Warning: Frame 2061 Coordinates out of bounds (-1)
	Warning: Frame 2078 Coordinates out of bounds (-1)
	Warning: Frame 2082 Coordinates out of bounds (-1)
	Warning: Frame 2155 Coordinates out of bounds (-1)
	Warning: Frame 2185 Coordinates out of bounds (-1)
	Warning: Frame 2201 Coordinates out of bounds (-1)
	Warning: Frame 2215 Coordinates out of bounds (-1)
	Warning: Frame 2227 Coordinates out of bounds (-1)
	Warning: Frame 2228 Coordinates out of bounds (-1)
	Warning: Frame 2230 Coordinates out of bounds (-1)
	Warning: Frame 2241 Coordinates out of bounds (-1)
	Warning: Frame 2272 Coordinates out of bounds (-1)
	Warning: Frame 2294 Coordinates out of bounds (-1)
	Warning: Frame 2412 Coordinates out of bounds (-1)
	Warning: Frame 2414 Coordinates out of bounds (-1)
	Warning: Frame 2430 Coordinates out of bounds (-1)
	Warning: Frame 2447 Coordinates out of bounds (-1)
	Warning: Frame 2457 Coordinates out of bounds (-1)
	Warning: Frame 2624 Coordinates out of bounds (-1)
	Warning: Frame 2639 Coordinates out of bounds (-1)
	Warning: Frame 2664 Coordinates out of bounds (-1)
	Warning: Frame 2684 Coordinates out of bounds (-1)
	Warning: Frame 2708 Coordinates out of bounds (-1)
	Warning: Frame 2767 Coordinates out of bounds (-1)
	Warning: Frame 2804 Coordinates out of bounds (-1)
	Warning: Frame 2839 Coordinates out of bounds (-1)
	Warning: Frame 2853 Coordinates out of bounds (-1)
	Warning: Frame 2860 Coordinates out of bounds (-1)
	Warning: Frame 2882 Coordinates out of bounds (-1)
	Warning: Frame 2904 Coordinates out of bounds (-1)
	Warning: Frame 2914 Coordinates out of bounds (-1)
	Warning: Frame 2916 Coordinates out of bounds (-1)
	Warning: Frame 2920 Coordinates out of bounds (-1)
	Warning: Frame 2927 Coordinates out of bounds (-1)
	Warning: Frame 2998 Coordinates out of bounds (-1)
	Warning: Frame 2999 Coordinates out of bounds (-1)
	Warning: Frame 3005 Coordinates out of bounds (-1)
	Warning: Frame 3021 Coordinates out of bounds (-1)
	Warning: Frame 3048 Coordinates out of bounds (-1)
	Warning: Frame 3080 Coordinates out of bounds (-1)
	Warning: Frame 3328 Coordinates out of bounds (-1)
	Warning: Frame 3331 Coordinates out of bounds (-1)
	Warning: Frame 3366 Coordinates out of bounds (-1)
	Warning: Frame 3368 Coordinates out of bounds (-1)
	Warning: Frame 3369 Coordinates out of bounds (-1)
	Warning: Frame 3424 Coordinates out of bounds (-1)
	Warning: Frame 3434 Coordinates out of bounds (-1)
	Warning: Frame 3435 Coordinates out of bounds (-1)
	Warning: Frame 3436 Coordinates out of bounds (-1)
	Warning: Frame 3454 Coordinates out of bounds (-1)
	Warning: Frame 3562 Coordinates out of bounds (-1)
	Warning: Frame 3616 Coordinates out of bounds (-1)
	Warning: Frame 3685 Coordinates out of bounds (-1)
	Warning: Frame 3735 Coordinates out of bounds (-1)
	Warning: Frame 3740 Coordinates out of bounds (-1)
	Warning: Frame 3780 Coordinates out of bounds (-1)
	Warning: Frame 3942 Coordinates out of bounds (-1)
	Warning: Frame 3975 Coordinates out of bounds (-1)
	Warning: Frame 3983 Coordinates out of bounds (-1)
	Warning: Frame 4065 Coordinates out of bounds (-1)
	Warning: Frame 4066 Coordinates out of bounds (-1)
	Warning: Frame 4067 Coordinates out of bounds (-1)
	Warning: Frame 4069 Coordinates out of bounds (-1)
	Warning: Frame 4074 Coordinates out of bounds (-1)
	Warning: Frame 4088 Coordinates out of bounds (-1)
	Warning: Frame 4126 Coordinates out of bounds (-1)
	Warning: Frame 4128 Coordinates out of bounds (-1)
	Warning: Frame 4157 Coordinates out of bounds (-1)
	Warning: Frame 4257 Coordinates out of bounds (-1)
	Warning: Frame 4304 Coordinates out of bounds (-1)
	Warning: Frame 4470 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 4343
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472
  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: 4472 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 4472

TIME: Analyses took 0.0018 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 4472
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 4472
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 4472
	COM "COM" (double, distance), size is 4472
	g1 "g1" (double, torsion(gamma)), size is 4472
	d1 "d1" (double, torsion(delta)), size is 4472
	e1 "e1" (double, torsion(epsilon)), size is 4472
	z1 "z1" (double, torsion(zeta)), size is 4472
	c1 "c1" (double, torsion(chin)), size is 4472
	a2 "a2" (double, torsion(alpha)), size is 4472
	b2 "b2" (double, torsion(beta)), size is 4472
	g2 "g2" (double, torsion(gamma)), size is 4472
	d2 "d2" (double, torsion(delta)), size is 4472
	c2 "c2" (double, torsion(chin)), size is 4472
	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 (  0.04%)
TIME:		Trajectory Process : 0.0101 s ( 17.98%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0018 s (  3.24%)
TIME:		Data File Write    : 0.0443 s ( 78.68%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0563 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1115 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.