CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:18:59
| Available memory: 7.198 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.c5]
	Reading '../ctraj.c5' 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, 60 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3835 of 3835)
  Coordinate processing will occur on 3835 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 7 donors:
	Imaging off.
	Estimated max potential memory usage: 9.576 kB
----- ctraj.c5 (1-3835, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 3835 frames and processed 3835 frames.
TIME: Avg. throughput= 160473.6798 frames / second.

ACTION OUTPUT:
    HBOND: Actual memory usage is 1.292 kB
	17 solute-solute hydrogen bonds.

DATASETS (1 total):
	HB_00001[UU] "HB_00001[UU]" (integer), size is 3835

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.07%)
TIME:		Trajectory Process : 0.0239 s ( 98.23%)
TIME:		Action Post        : 0.0004 s (  1.53%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.04%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.0243 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0361 seconds.
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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.