CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16  11:36:53
| Available memory: 8363.64 MB

INPUT: Reading Input from file pt-hb-rna.in
  [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
	Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
  [autoimage origin]
    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:
 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 6109 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 6109 of 6109)
  Coordinate processing will occur on 6109 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (3 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  2: [hbond :1-2 avgout avghb-rna.dat printatomnum]
	Set up 20 acceptors:
	Set up 8 donors:
	Imaging off.
	Estimated max potential memory usage: 0.01 MB
----- ctraj.c5 (1-6109, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 6109 frames and processed 6109 frames.
TIME: Trajectory processing: 1.0444 s
TIME: Avg. throughput= 5849.2747 frames / second.

ACTION OUTPUT:
    HBOND: Actual memory usage is 0.00 MB
	23 solute-solute hydrogen bonds.

DATASETS:
  1 data set:
	HB_00000[UU] "HB_00000[UU]" (integer), size is 6109

DATAFILES:
  avghb-rna.dat (Avg. solute-solute HBonds)
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.0629 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.