CPPTRAJ: Trajectory Analysis. V16.00b
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 06/03/16 11:08:53
| Available memory: 1.891 GB

INPUT: Reading input from 'pt-hb-rna.in'
  [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]]
	Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [autoimage origin]
Warning: Action specified before trajin/ensemble. Assuming trajin.
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [trajin ../ctraj.c2]
	Reading '../ctraj.c2' as Amber NetCDF
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [hbond :1-2 avgout avghb-rna.dat printatomnum]
  HBOND: Searching for Hbond donors/acceptors in region specified by :1-2
	Distance cutoff = 3.000, Angle Cutoff = 135.000
	Writing Hbond avgs to avghb-rna.dat
	Atom numbers will be written to output.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: [traj] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 59196 of 59196)
  Coordinate processing will occur on 59196 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (3 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [hbond :1-2 avgout avghb-rna.dat printatomnum]
	Set up 18 acceptors:
	Set up 8 donors:
	Imaging off.
	Estimated max potential memory usage: 10.944 kB
----- ctraj.c2 (1-59196, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 59196 frames and processed 59196 frames.
TIME: Avg. throughput= 156311.6410 frames / second.

ACTION OUTPUT:
    HBOND: Actual memory usage is 1.976 kB
	26 solute-solute hydrogen bonds.

DATASETS (1 total):
	HB_00001[UU] "HB_00001[UU]" (integer), size is 59196

DATAFILES (1 total):
  avghb-rna.dat (Avg. solute-solute HBonds)

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.01%)
TIME:		Trajectory Process : 0.3787 s ( 99.85%)
TIME:		Action Post        : 0.0005 s (  0.13%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.3793 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.3901 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.