CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/04/15 11:11:04
| Available memory: 802.488 MB

INPUT: Reading Input from file pt-analysis1.in
  [parm ../../../build/noWAt.topo.hmr]
	Reading '../../../build/noWAt.topo.hmr' as Amber Topology
  [trajin trig.nc]
	Reading 'trig.nc' 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]
	Reference mask: [:1,2&!@H*](43)
    RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted.
  [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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, 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 chin]
    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@N9 :2@C4 type chin]
    DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4]
              Output range is -180 to 180 degrees.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES:
 0: 'trig.nc' is a NetCDF AMBER trajectory with replica temperatures, Parm noWAt.topo.hmr (Orthogonal box) (reading 10222 of 10222)
  Coordinate processing will occur on 10222 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'
TIME: Run Initialization took 0.0000 seconds.

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*](43)
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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 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 chin]
	 [: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@N9 :2@C4 type chin]
	 [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- trig.nc (1-10222, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 10222 frames and processed 10222 frames.
TIME: Trajectory processing: 0.1057 s
TIME: Avg. throughput= 96731.4571 frames / second.

ACTION OUTPUT:

DATASETS:
  16 data sets:
	noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
	[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms
	rms_2_aform "rms_2_aform" (double, rms), size is 10222
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 10222
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 10222
	COM "COM" (double, distance), size is 10222
	g1 "g1" (double, torsion(gamma)), size is 10222
	d1 "d1" (double, torsion(delta)), size is 10222
	e1 "e1" (double, torsion(epsilon)), size is 10222
	z1 "z1" (double, torsion(zeta)), size is 10222
	c1 "c1" (double, torsion(chin)), size is 10222
	a2 "a2" (double, torsion(alpha)), size is 10222
	b2 "b2" (double, torsion(beta)), size is 10222
	g2 "g2" (double, torsion(gamma)), size is 10222
	d2 "d2" (double, torsion(delta)), size is 10222
	c2 "c2" (double, torsion(chin)), size is 10222
---------- RUN END ---------------------------------------------------
  [avg rms_2_aform out avg-rmsd-all.dat]
    AVERAGE: Calculating average of 1 data sets.
	Writing results 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 -------------------------------------------------
Warning: No actions/output trajectories specified.

ANALYSIS: Performing 16 analyses:
  0: [avg rms_2_aform out avg-rmsd-all.dat]
  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: 10222 data points in each dimension.
	Hist: Allocating histogram, total bins = 50
	Warning: Frame 1646 Coordinates out of bounds (-1)
	Warning: Frame 1657 Coordinates out of bounds (-1)
	Warning: Frame 1663 Coordinates out of bounds (-1)
	Warning: Frame 2536 Coordinates out of bounds (-1)
	Warning: Frame 3207 Coordinates out of bounds (-1)
	Warning: Frame 4411 Coordinates out of bounds (-1)
	Warning: Frame 5174 Coordinates out of bounds (-1)
	Warning: Frame 5401 Coordinates out of bounds (-1)
	Warning: Frame 6728 Coordinates out of bounds (-1)
	Warning: Frame 6818 Coordinates out of bounds (-1)
	Warning: Frame 8771 Coordinates out of bounds (-1)
	Warning: Frame 8776 Coordinates out of bounds (-1)
	Warning: Frame 8786 Coordinates out of bounds (-1)
	Warning: Frame 9093 Coordinates out of bounds (-1)
	Warning: Frame 9223 Coordinates out of bounds (-1)
	Warning: Frame 9486 Coordinates out of bounds (-1)
	Warning: Frame 9897 Coordinates out of bounds (-1)
	Warning: Frame 9899 Coordinates out of bounds (-1)
	Warning: Frame 10156 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 10203
  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: 10222 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 28 Coordinates out of bounds (-1)
	Warning: Frame 34 Coordinates out of bounds (-1)
	Warning: Frame 35 Coordinates out of bounds (-1)
	Warning: Frame 39 Coordinates out of bounds (-1)
	Warning: Frame 64 Coordinates out of bounds (-1)
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	Warning: Frame 164 Coordinates out of bounds (-1)
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	Warning: Frame 9763 Coordinates out of bounds (-1)
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	Warning: Frame 9869 Coordinates out of bounds (-1)
	Warning: Frame 9870 Coordinates out of bounds (-1)
	Warning: Frame 9874 Coordinates out of bounds (-1)
	Warning: Frame 9897 Coordinates out of bounds (-1)
	Warning: Frame 9898 Coordinates out of bounds (-1)
	Warning: Frame 9899 Coordinates out of bounds (-1)
	Warning: Frame 9900 Coordinates out of bounds (-1)
	Warning: Frame 9903 Coordinates out of bounds (-1)
	Warning: Frame 9904 Coordinates out of bounds (-1)
	Warning: Frame 9909 Coordinates out of bounds (-1)
	Warning: Frame 9911 Coordinates out of bounds (-1)
	Warning: Frame 9918 Coordinates out of bounds (-1)
	Warning: Frame 9997 Coordinates out of bounds (-1)
	Warning: Frame 9998 Coordinates out of bounds (-1)
	Warning: Frame 10063 Coordinates out of bounds (-1)
	Warning: Frame 10064 Coordinates out of bounds (-1)
	Warning: Frame 10066 Coordinates out of bounds (-1)
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	Warning: Frame 10156 Coordinates out of bounds (-1)
	Warning: Frame 10158 Coordinates out of bounds (-1)
	Warning: Frame 10160 Coordinates out of bounds (-1)
	Warning: Frame 10162 Coordinates out of bounds (-1)
	Warning: Frame 10163 Coordinates out of bounds (-1)
	Warning: Frame 10182 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 9859
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 data points in each dimension.
	Hist: Allocating histogram, total bins = 5000
	Warning: Frame 1646 Coordinates out of bounds (-1)
	Warning: Frame 1657 Coordinates out of bounds (-1)
	Warning: Frame 1663 Coordinates out of bounds (-1)
	Warning: Frame 2536 Coordinates out of bounds (-1)
	Warning: Frame 3207 Coordinates out of bounds (-1)
	Warning: Frame 4411 Coordinates out of bounds (-1)
	Warning: Frame 5174 Coordinates out of bounds (-1)
	Warning: Frame 5401 Coordinates out of bounds (-1)
	Warning: Frame 6728 Coordinates out of bounds (-1)
	Warning: Frame 6818 Coordinates out of bounds (-1)
	Warning: Frame 8771 Coordinates out of bounds (-1)
	Warning: Frame 8776 Coordinates out of bounds (-1)
	Warning: Frame 8786 Coordinates out of bounds (-1)
	Warning: Frame 9093 Coordinates out of bounds (-1)
	Warning: Frame 9223 Coordinates out of bounds (-1)
	Warning: Frame 9486 Coordinates out of bounds (-1)
	Warning: Frame 9897 Coordinates out of bounds (-1)
	Warning: Frame 9899 Coordinates out of bounds (-1)
	Warning: Frame 10156 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 10203
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222
  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: 10222 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 10222

TIME: Analyses took 0.0040 seconds.

DATASETS:
  31 data sets:
	noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
	[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms
	rms_2_aform "rms_2_aform" (double, rms), size is 10222
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 10222
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 10222
	COM "COM" (double, distance), size is 10222
	g1 "g1" (double, torsion(gamma)), size is 10222
	d1 "d1" (double, torsion(delta)), size is 10222
	e1 "e1" (double, torsion(epsilon)), size is 10222
	z1 "z1" (double, torsion(zeta)), size is 10222
	c1 "c1" (double, torsion(chin)), size is 10222
	a2 "a2" (double, torsion(alpha)), size is 10222
	b2 "b2" (double, torsion(beta)), size is 10222
	g2 "g2" (double, torsion(gamma)), size is 10222
	d2 "d2" (double, torsion(delta)), size is 10222
	c2 "c2" (double, torsion(chin)), size is 10222
	RMSD "RMSD" (double), size is 50
	CoM "CoM" (double), size is 100
	Hist_00018 "Hist_00018" (double), size is 100
	Hist_00019 "Hist_00019" (double), size is 100
	Hist_00020 "Hist_00020" (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:
  rmsd-hist.dat (Standard Data File):  RMSD
  COM-hist.dat (Standard Data File):  CoM
  distO2O4-hist.dat (Standard Data File):  Hist_00018
  distN3-O5p-hist.dat (Standard Data File):  Hist_00019
  2dhist_rms-dist.gnu (Gnuplot File):  Hist_00020
  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
  avg-rmsd-all.dat (DataSet Average)
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1658 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.