CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:18:58
| Available memory: 7.207 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.c3]
	Reading '../ctraj.c3' 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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8410 of 8410)
  Coordinate processing will occur on 8410 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.c3 (1-8410, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 8410 frames and processed 8410 frames.
TIME: Avg. throughput= 108994.2976 frames / second.

ACTION OUTPUT:

DATASETS (14 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 8410
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 8410
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 8410
	COM "COM" (double, distance), size is 8410
	g1 "g1" (double, torsion(gamma)), size is 8410
	d1 "d1" (double, torsion(delta)), size is 8410
	e1 "e1" (double, torsion(epsilon)), size is 8410
	z1 "z1" (double, torsion(zeta)), size is 8410
	c1 "c1" (double, torsion(chin)), size is 8410
	a2 "a2" (double, torsion(alpha)), size is 8410
	b2 "b2" (double, torsion(beta)), size is 8410
	g2 "g2" (double, torsion(gamma)), size is 8410
	d2 "d2" (double, torsion(delta)), size is 8410
	c2 "c2" (double, torsion(chin)), size is 8410

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.05%)
TIME:		Trajectory Process : 0.0772 s ( 99.83%)
TIME:		Action Post        : 0.0000 s (  0.01%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.05%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0773 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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8410 of 8410)
  Coordinate processing will occur on 8410 frames.

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

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c3 (1-8410, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 8410 frames and processed 8410 frames.
TIME: Avg. throughput= 417992.0477 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: 8410 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 8410
  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: 8410 data points in each dimension.
	Hist: Allocating histogram, total bins = 100
	Warning: Frame 21 Coordinates out of bounds (-1)
	Warning: Frame 79 Coordinates out of bounds (-1)
	Warning: Frame 144 Coordinates out of bounds (-1)
	Warning: Frame 157 Coordinates out of bounds (-1)
	Warning: Frame 235 Coordinates out of bounds (-1)
	Warning: Frame 248 Coordinates out of bounds (-1)
	Warning: Frame 251 Coordinates out of bounds (-1)
	Warning: Frame 252 Coordinates out of bounds (-1)
	Warning: Frame 366 Coordinates out of bounds (-1)
	Warning: Frame 367 Coordinates out of bounds (-1)
	Warning: Frame 467 Coordinates out of bounds (-1)
	Warning: Frame 595 Coordinates out of bounds (-1)
	Warning: Frame 596 Coordinates out of bounds (-1)
	Warning: Frame 600 Coordinates out of bounds (-1)
	Warning: Frame 605 Coordinates out of bounds (-1)
	Warning: Frame 658 Coordinates out of bounds (-1)
	Warning: Frame 858 Coordinates out of bounds (-1)
	Warning: Frame 860 Coordinates out of bounds (-1)
	Warning: Frame 878 Coordinates out of bounds (-1)
	Warning: Frame 897 Coordinates out of bounds (-1)
	Warning: Frame 1079 Coordinates out of bounds (-1)
	Warning: Frame 1101 Coordinates out of bounds (-1)
	Warning: Frame 1151 Coordinates out of bounds (-1)
	Warning: Frame 1357 Coordinates out of bounds (-1)
	Warning: Frame 1361 Coordinates out of bounds (-1)
	Warning: Frame 1421 Coordinates out of bounds (-1)
	Warning: Frame 1442 Coordinates out of bounds (-1)
	Warning: Frame 1514 Coordinates out of bounds (-1)
	Warning: Frame 1700 Coordinates out of bounds (-1)
	Warning: Frame 1720 Coordinates out of bounds (-1)
	Warning: Frame 1764 Coordinates out of bounds (-1)
	Warning: Frame 1779 Coordinates out of bounds (-1)
	Warning: Frame 1791 Coordinates out of bounds (-1)
	Warning: Frame 1832 Coordinates out of bounds (-1)
	Warning: Frame 1914 Coordinates out of bounds (-1)
	Warning: Frame 2032 Coordinates out of bounds (-1)
	Warning: Frame 2038 Coordinates out of bounds (-1)
	Warning: Frame 2097 Coordinates out of bounds (-1)
	Warning: Frame 2146 Coordinates out of bounds (-1)
	Warning: Frame 2234 Coordinates out of bounds (-1)
	Warning: Frame 2262 Coordinates out of bounds (-1)
	Warning: Frame 2282 Coordinates out of bounds (-1)
	Warning: Frame 2293 Coordinates out of bounds (-1)
	Warning: Frame 2294 Coordinates out of bounds (-1)
	Warning: Frame 2327 Coordinates out of bounds (-1)
	Warning: Frame 2402 Coordinates out of bounds (-1)
	Warning: Frame 2444 Coordinates out of bounds (-1)
	Warning: Frame 2614 Coordinates out of bounds (-1)
	Warning: Frame 2620 Coordinates out of bounds (-1)
	Warning: Frame 2653 Coordinates out of bounds (-1)
	Warning: Frame 2752 Coordinates out of bounds (-1)
	Warning: Frame 2775 Coordinates out of bounds (-1)
	Warning: Frame 2916 Coordinates out of bounds (-1)
	Warning: Frame 2976 Coordinates out of bounds (-1)
	Warning: Frame 3178 Coordinates out of bounds (-1)
	Warning: Frame 3231 Coordinates out of bounds (-1)
	Warning: Frame 3297 Coordinates out of bounds (-1)
	Warning: Frame 3338 Coordinates out of bounds (-1)
	Warning: Frame 3356 Coordinates out of bounds (-1)
	Warning: Frame 3365 Coordinates out of bounds (-1)
	Warning: Frame 3370 Coordinates out of bounds (-1)
	Warning: Frame 3371 Coordinates out of bounds (-1)
	Warning: Frame 3372 Coordinates out of bounds (-1)
	Warning: Frame 3416 Coordinates out of bounds (-1)
	Warning: Frame 3420 Coordinates out of bounds (-1)
	Warning: Frame 3447 Coordinates out of bounds (-1)
	Warning: Frame 3504 Coordinates out of bounds (-1)
	Warning: Frame 3505 Coordinates out of bounds (-1)
	Warning: Frame 3575 Coordinates out of bounds (-1)
	Warning: Frame 3582 Coordinates out of bounds (-1)
	Warning: Frame 3583 Coordinates out of bounds (-1)
	Warning: Frame 3597 Coordinates out of bounds (-1)
	Warning: Frame 3624 Coordinates out of bounds (-1)
	Warning: Frame 3627 Coordinates out of bounds (-1)
	Warning: Frame 3639 Coordinates out of bounds (-1)
	Warning: Frame 3705 Coordinates out of bounds (-1)
	Warning: Frame 3739 Coordinates out of bounds (-1)
	Warning: Frame 3788 Coordinates out of bounds (-1)
	Warning: Frame 3835 Coordinates out of bounds (-1)
	Warning: Frame 3924 Coordinates out of bounds (-1)
	Warning: Frame 3949 Coordinates out of bounds (-1)
	Warning: Frame 3950 Coordinates out of bounds (-1)
	Warning: Frame 4122 Coordinates out of bounds (-1)
	Warning: Frame 4180 Coordinates out of bounds (-1)
	Warning: Frame 4288 Coordinates out of bounds (-1)
	Warning: Frame 4320 Coordinates out of bounds (-1)
	Warning: Frame 4371 Coordinates out of bounds (-1)
	Warning: Frame 4404 Coordinates out of bounds (-1)
	Warning: Frame 4409 Coordinates out of bounds (-1)
	Warning: Frame 4484 Coordinates out of bounds (-1)
	Warning: Frame 4530 Coordinates out of bounds (-1)
	Warning: Frame 4650 Coordinates out of bounds (-1)
	Warning: Frame 4678 Coordinates out of bounds (-1)
	Warning: Frame 4712 Coordinates out of bounds (-1)
	Warning: Frame 4819 Coordinates out of bounds (-1)
	Warning: Frame 4898 Coordinates out of bounds (-1)
	Warning: Frame 4943 Coordinates out of bounds (-1)
	Warning: Frame 4949 Coordinates out of bounds (-1)
	Warning: Frame 4968 Coordinates out of bounds (-1)
	Warning: Frame 4988 Coordinates out of bounds (-1)
	Warning: Frame 5011 Coordinates out of bounds (-1)
	Warning: Frame 5012 Coordinates out of bounds (-1)
	Warning: Frame 5174 Coordinates out of bounds (-1)
	Warning: Frame 5205 Coordinates out of bounds (-1)
	Warning: Frame 5229 Coordinates out of bounds (-1)
	Warning: Frame 5395 Coordinates out of bounds (-1)
	Warning: Frame 5438 Coordinates out of bounds (-1)
	Warning: Frame 5464 Coordinates out of bounds (-1)
	Warning: Frame 5465 Coordinates out of bounds (-1)
	Warning: Frame 5474 Coordinates out of bounds (-1)
	Warning: Frame 5482 Coordinates out of bounds (-1)
	Warning: Frame 5495 Coordinates out of bounds (-1)
	Warning: Frame 5496 Coordinates out of bounds (-1)
	Warning: Frame 5566 Coordinates out of bounds (-1)
	Warning: Frame 5653 Coordinates out of bounds (-1)
	Warning: Frame 5684 Coordinates out of bounds (-1)
	Warning: Frame 5685 Coordinates out of bounds (-1)
	Warning: Frame 5707 Coordinates out of bounds (-1)
	Warning: Frame 5803 Coordinates out of bounds (-1)
	Warning: Frame 5810 Coordinates out of bounds (-1)
	Warning: Frame 5988 Coordinates out of bounds (-1)
	Warning: Frame 6078 Coordinates out of bounds (-1)
	Warning: Frame 6104 Coordinates out of bounds (-1)
	Warning: Frame 6129 Coordinates out of bounds (-1)
	Warning: Frame 6176 Coordinates out of bounds (-1)
	Warning: Frame 6231 Coordinates out of bounds (-1)
	Warning: Frame 6243 Coordinates out of bounds (-1)
	Warning: Frame 6256 Coordinates out of bounds (-1)
	Warning: Frame 6262 Coordinates out of bounds (-1)
	Warning: Frame 6270 Coordinates out of bounds (-1)
	Warning: Frame 6466 Coordinates out of bounds (-1)
	Warning: Frame 6504 Coordinates out of bounds (-1)
	Warning: Frame 6643 Coordinates out of bounds (-1)
	Warning: Frame 6644 Coordinates out of bounds (-1)
	Warning: Frame 6897 Coordinates out of bounds (-1)
	Warning: Frame 6898 Coordinates out of bounds (-1)
	Warning: Frame 6932 Coordinates out of bounds (-1)
	Warning: Frame 6995 Coordinates out of bounds (-1)
	Warning: Frame 7014 Coordinates out of bounds (-1)
	Warning: Frame 7018 Coordinates out of bounds (-1)
	Warning: Frame 7105 Coordinates out of bounds (-1)
	Warning: Frame 7125 Coordinates out of bounds (-1)
	Warning: Frame 7368 Coordinates out of bounds (-1)
	Warning: Frame 7386 Coordinates out of bounds (-1)
	Warning: Frame 7394 Coordinates out of bounds (-1)
	Warning: Frame 7483 Coordinates out of bounds (-1)
	Warning: Frame 7610 Coordinates out of bounds (-1)
	Warning: Frame 7710 Coordinates out of bounds (-1)
	Warning: Frame 7757 Coordinates out of bounds (-1)
	Warning: Frame 7758 Coordinates out of bounds (-1)
	Warning: Frame 7805 Coordinates out of bounds (-1)
	Warning: Frame 7811 Coordinates out of bounds (-1)
	Warning: Frame 7974 Coordinates out of bounds (-1)
	Warning: Frame 8004 Coordinates out of bounds (-1)
	Warning: Frame 8163 Coordinates out of bounds (-1)
	Warning: Frame 8171 Coordinates out of bounds (-1)
	Warning: Frame 8172 Coordinates out of bounds (-1)
	Warning: Frame 8184 Coordinates out of bounds (-1)
	Warning: Frame 8248 Coordinates out of bounds (-1)
	Warning: Frame 8301 Coordinates out of bounds (-1)
	Warning: Frame 8305 Coordinates out of bounds (-1)
	Warning: Frame 8319 Coordinates out of bounds (-1)
	Warning: Frame 8410 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 8247
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410
  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: 8410 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 8410

TIME: Analyses took 0.0030 seconds.

DATASETS (36 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 8410
	dist_sugar_ox "dist_sugar_ox" (double, distance), size is 8410
	dist_N3-O5p "dist_N3-O5p" (double, distance), size is 8410
	COM "COM" (double, distance), size is 8410
	g1 "g1" (double, torsion(gamma)), size is 8410
	d1 "d1" (double, torsion(delta)), size is 8410
	e1 "e1" (double, torsion(epsilon)), size is 8410
	z1 "z1" (double, torsion(zeta)), size is 8410
	c1 "c1" (double, torsion(chin)), size is 8410
	a2 "a2" (double, torsion(alpha)), size is 8410
	b2 "b2" (double, torsion(beta)), size is 8410
	g2 "g2" (double, torsion(gamma)), size is 8410
	d2 "d2" (double, torsion(delta)), size is 8410
	c2 "c2" (double, torsion(chin)), size is 8410
	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 (  0.05%)
TIME:		Trajectory Process : 0.0201 s ( 40.21%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0030 s (  6.06%)
TIME:		Data File Write    : 0.0268 s ( 53.58%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0500 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1424 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.