CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 16:43:59
| Available memory: 3.941 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,N4,H41,H42,N3,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,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@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, 64 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 18419 of 18419)
  Coordinate processing will occur on 18419 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,N4,H41,H42,N3,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,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@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 (1-18419, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 18419 frames and processed 18419 frames.
TIME: Avg. throughput= 104226.4360 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 18419
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 18419
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 18419
	COM "COM" (double, distance), size is 18419
	g1 "g1" (double, torsion(gamma)), size is 18419
	d1 "d1" (double, torsion(delta)), size is 18419
	e1 "e1" (double, torsion(epsilon)), size is 18419
	z1 "z1" (double, torsion(zeta)), size is 18419
	c1 "c1" (double, torsion(chin)), size is 18419
	a2 "a2" (double, torsion(alpha)), size is 18419
	b2 "b2" (double, torsion(beta)), size is 18419
	g2 "g2" (double, torsion(gamma)), size is 18419
	d2 "d2" (double, torsion(delta)), size is 18419
	c2 "c2" (double, torsion(chin)), size is 18419

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.1767 s ( 99.94%)
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 0.1768 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18419 of 18419)
  Coordinate processing will occur on 18419 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 (1-18419, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 18419 frames and processed 18419 frames.
TIME: Avg. throughput= 402724.3309 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: 18419 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 18419
  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: 18419 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 226 Coordinates out of bounds (-1)
	Warning: Frame 250 Coordinates out of bounds (-1)
	Warning: Frame 252 Coordinates out of bounds (-1)
	Warning: Frame 253 Coordinates out of bounds (-1)
	Warning: Frame 254 Coordinates out of bounds (-1)
	Warning: Frame 255 Coordinates out of bounds (-1)
	Warning: Frame 270 Coordinates out of bounds (-1)
	Warning: Frame 611 Coordinates out of bounds (-1)
	Warning: Frame 612 Coordinates out of bounds (-1)
	Warning: Frame 700 Coordinates out of bounds (-1)
	Warning: Frame 706 Coordinates out of bounds (-1)
	Warning: Frame 884 Coordinates out of bounds (-1)
	Warning: Frame 1275 Coordinates out of bounds (-1)
	Warning: Frame 1332 Coordinates out of bounds (-1)
	Warning: Frame 1707 Coordinates out of bounds (-1)
	Warning: Frame 1708 Coordinates out of bounds (-1)
	Warning: Frame 2065 Coordinates out of bounds (-1)
	Warning: Frame 2547 Coordinates out of bounds (-1)
	Warning: Frame 2901 Coordinates out of bounds (-1)
	Warning: Frame 2902 Coordinates out of bounds (-1)
	Warning: Frame 2903 Coordinates out of bounds (-1)
	Warning: Frame 3174 Coordinates out of bounds (-1)
	Warning: Frame 3308 Coordinates out of bounds (-1)
	Warning: Frame 3311 Coordinates out of bounds (-1)
	Warning: Frame 3317 Coordinates out of bounds (-1)
	Warning: Frame 3423 Coordinates out of bounds (-1)
	Warning: Frame 3664 Coordinates out of bounds (-1)
	Warning: Frame 3796 Coordinates out of bounds (-1)
	Warning: Frame 3799 Coordinates out of bounds (-1)
	Warning: Frame 3800 Coordinates out of bounds (-1)
	Warning: Frame 3801 Coordinates out of bounds (-1)
	Warning: Frame 3802 Coordinates out of bounds (-1)
	Warning: Frame 3803 Coordinates out of bounds (-1)
	Warning: Frame 4415 Coordinates out of bounds (-1)
	Warning: Frame 4560 Coordinates out of bounds (-1)
	Warning: Frame 4565 Coordinates out of bounds (-1)
	Warning: Frame 4769 Coordinates out of bounds (-1)
	Warning: Frame 4775 Coordinates out of bounds (-1)
	Warning: Frame 5006 Coordinates out of bounds (-1)
	Warning: Frame 5509 Coordinates out of bounds (-1)
	Warning: Frame 5510 Coordinates out of bounds (-1)
	Warning: Frame 5535 Coordinates out of bounds (-1)
	Warning: Frame 6038 Coordinates out of bounds (-1)
	Warning: Frame 6492 Coordinates out of bounds (-1)
	Warning: Frame 6627 Coordinates out of bounds (-1)
	Warning: Frame 6629 Coordinates out of bounds (-1)
	Warning: Frame 6646 Coordinates out of bounds (-1)
	Warning: Frame 6649 Coordinates out of bounds (-1)
	Warning: Frame 6745 Coordinates out of bounds (-1)
	Warning: Frame 6925 Coordinates out of bounds (-1)
	Warning: Frame 7025 Coordinates out of bounds (-1)
	Warning: Frame 7030 Coordinates out of bounds (-1)
	Warning: Frame 7483 Coordinates out of bounds (-1)
	Warning: Frame 7833 Coordinates out of bounds (-1)
	Warning: Frame 7988 Coordinates out of bounds (-1)
	Warning: Frame 7989 Coordinates out of bounds (-1)
	Warning: Frame 7990 Coordinates out of bounds (-1)
	Warning: Frame 7992 Coordinates out of bounds (-1)
	Warning: Frame 7998 Coordinates out of bounds (-1)
	Warning: Frame 8609 Coordinates out of bounds (-1)
	Warning: Frame 8670 Coordinates out of bounds (-1)
	Warning: Frame 8782 Coordinates out of bounds (-1)
	Warning: Frame 8783 Coordinates out of bounds (-1)
	Warning: Frame 8785 Coordinates out of bounds (-1)
	Warning: Frame 8793 Coordinates out of bounds (-1)
	Warning: Frame 8794 Coordinates out of bounds (-1)
	Warning: Frame 9003 Coordinates out of bounds (-1)
	Warning: Frame 9424 Coordinates out of bounds (-1)
	Warning: Frame 9671 Coordinates out of bounds (-1)
	Warning: Frame 9692 Coordinates out of bounds (-1)
	Warning: Frame 9694 Coordinates out of bounds (-1)
	Warning: Frame 10004 Coordinates out of bounds (-1)
	Warning: Frame 10005 Coordinates out of bounds (-1)
	Warning: Frame 10081 Coordinates out of bounds (-1)
	Warning: Frame 10298 Coordinates out of bounds (-1)
	Warning: Frame 10345 Coordinates out of bounds (-1)
	Warning: Frame 10496 Coordinates out of bounds (-1)
	Warning: Frame 10668 Coordinates out of bounds (-1)
	Warning: Frame 11315 Coordinates out of bounds (-1)
	Warning: Frame 11332 Coordinates out of bounds (-1)
	Warning: Frame 11365 Coordinates out of bounds (-1)
	Warning: Frame 11507 Coordinates out of bounds (-1)
	Warning: Frame 11508 Coordinates out of bounds (-1)
	Warning: Frame 11550 Coordinates out of bounds (-1)
	Warning: Frame 11557 Coordinates out of bounds (-1)
	Warning: Frame 12041 Coordinates out of bounds (-1)
	Warning: Frame 12106 Coordinates out of bounds (-1)
	Warning: Frame 12333 Coordinates out of bounds (-1)
	Warning: Frame 12518 Coordinates out of bounds (-1)
	Warning: Frame 12602 Coordinates out of bounds (-1)
	Warning: Frame 12631 Coordinates out of bounds (-1)
	Warning: Frame 12646 Coordinates out of bounds (-1)
	Warning: Frame 12806 Coordinates out of bounds (-1)
	Warning: Frame 12914 Coordinates out of bounds (-1)
	Warning: Frame 12915 Coordinates out of bounds (-1)
	Warning: Frame 13002 Coordinates out of bounds (-1)
	Warning: Frame 13005 Coordinates out of bounds (-1)
	Warning: Frame 13022 Coordinates out of bounds (-1)
	Warning: Frame 13025 Coordinates out of bounds (-1)
	Warning: Frame 13026 Coordinates out of bounds (-1)
	Warning: Frame 13165 Coordinates out of bounds (-1)
	Warning: Frame 13308 Coordinates out of bounds (-1)
	Warning: Frame 13514 Coordinates out of bounds (-1)
	Warning: Frame 13515 Coordinates out of bounds (-1)
	Warning: Frame 13516 Coordinates out of bounds (-1)
	Warning: Frame 13533 Coordinates out of bounds (-1)
	Warning: Frame 13854 Coordinates out of bounds (-1)
	Warning: Frame 13971 Coordinates out of bounds (-1)
	Warning: Frame 13978 Coordinates out of bounds (-1)
	Warning: Frame 14002 Coordinates out of bounds (-1)
	Warning: Frame 14011 Coordinates out of bounds (-1)
	Warning: Frame 14014 Coordinates out of bounds (-1)
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	Warning: Frame 14134 Coordinates out of bounds (-1)
	Warning: Frame 14159 Coordinates out of bounds (-1)
	Warning: Frame 14234 Coordinates out of bounds (-1)
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	Warning: Frame 14394 Coordinates out of bounds (-1)
	Warning: Frame 14636 Coordinates out of bounds (-1)
	Warning: Frame 14638 Coordinates out of bounds (-1)
	Warning: Frame 14643 Coordinates out of bounds (-1)
	Warning: Frame 14855 Coordinates out of bounds (-1)
	Warning: Frame 15074 Coordinates out of bounds (-1)
	Warning: Frame 15075 Coordinates out of bounds (-1)
	Warning: Frame 15076 Coordinates out of bounds (-1)
	Warning: Frame 15518 Coordinates out of bounds (-1)
	Warning: Frame 16241 Coordinates out of bounds (-1)
	Warning: Frame 16242 Coordinates out of bounds (-1)
	Warning: Frame 16243 Coordinates out of bounds (-1)
	Warning: Frame 16244 Coordinates out of bounds (-1)
	Warning: Frame 16252 Coordinates out of bounds (-1)
	Warning: Frame 16413 Coordinates out of bounds (-1)
	Warning: Frame 16414 Coordinates out of bounds (-1)
	Warning: Frame 16500 Coordinates out of bounds (-1)
	Warning: Frame 16501 Coordinates out of bounds (-1)
	Warning: Frame 16557 Coordinates out of bounds (-1)
	Warning: Frame 16558 Coordinates out of bounds (-1)
	Warning: Frame 16559 Coordinates out of bounds (-1)
	Warning: Frame 16614 Coordinates out of bounds (-1)
	Warning: Frame 16615 Coordinates out of bounds (-1)
	Warning: Frame 16801 Coordinates out of bounds (-1)
	Warning: Frame 16803 Coordinates out of bounds (-1)
	Warning: Frame 16805 Coordinates out of bounds (-1)
	Warning: Frame 16851 Coordinates out of bounds (-1)
	Warning: Frame 16852 Coordinates out of bounds (-1)
	Warning: Frame 16853 Coordinates out of bounds (-1)
	Warning: Frame 16879 Coordinates out of bounds (-1)
	Warning: Frame 16880 Coordinates out of bounds (-1)
	Warning: Frame 16949 Coordinates out of bounds (-1)
	Warning: Frame 17059 Coordinates out of bounds (-1)
	Warning: Frame 17182 Coordinates out of bounds (-1)
	Warning: Frame 17183 Coordinates out of bounds (-1)
	Warning: Frame 17499 Coordinates out of bounds (-1)
	Warning: Frame 17667 Coordinates out of bounds (-1)
	Warning: Frame 17866 Coordinates out of bounds (-1)
	Warning: Frame 17868 Coordinates out of bounds (-1)
	Warning: Frame 17870 Coordinates out of bounds (-1)
	Warning: Frame 17911 Coordinates out of bounds (-1)
	Warning: Frame 18038 Coordinates out of bounds (-1)
	Warning: Frame 18048 Coordinates out of bounds (-1)
	Warning: Frame 18364 Coordinates out of bounds (-1)
	Warning: Frame 18368 Coordinates out of bounds (-1)
	Warning: Frame 18369 Coordinates out of bounds (-1)
	Warning: Frame 18372 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 18255
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419
  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: 18419 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 18419

TIME: Analyses took 0.0064 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 18419
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 18419
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 18419
	COM "COM" (double, distance), size is 18419
	g1 "g1" (double, torsion(gamma)), size is 18419
	d1 "d1" (double, torsion(delta)), size is 18419
	e1 "e1" (double, torsion(epsilon)), size is 18419
	z1 "z1" (double, torsion(zeta)), size is 18419
	c1 "c1" (double, torsion(chin)), size is 18419
	a2 "a2" (double, torsion(alpha)), size is 18419
	b2 "b2" (double, torsion(beta)), size is 18419
	g2 "g2" (double, torsion(gamma)), size is 18419
	d2 "d2" (double, torsion(delta)), size is 18419
	c2 "c2" (double, torsion(chin)), size is 18419
	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 : 0.0457 s (  5.76%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0064 s (  0.81%)
TIME:		Data File Write    : 0.7420 s ( 93.43%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.7942 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.4478 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.