CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/07/16 18:04:00
| Available memory: 1.373 GB

INPUT: Reading input from 'pt-hb-rna.in'
  [parm ../../build/full.topo.hmr [traj]]
	Reading '../../build/full.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 ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,]
	Reading '../../traj.1.01' 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] full.topo.hmr, 3302 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent

INPUT TRAJECTORIES (1 total):
 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
  Coordinate processing will occur on 50000 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (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 21 acceptors:
	Set up 9 donors:
	Imaging off.
	Estimated max potential memory usage: 14.364 kB
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 50000 frames and processed 50000 frames.
TIME: Avg. throughput= 58.0226 frames / second.

ACTION OUTPUT:
    HBOND: Actual memory usage is 4.408 kB
	58 solute-solute hydrogen bonds.

DATASETS (1 total):
	HB_00001[UU] "HB_00001[UU]" (integer), size is 50000

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.00%)
TIME:		Trajectory Process : 861.7336 s ( 99.98%)
TIME:		Action Post        : 0.1413 s (  0.02%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 861.8750 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 884.7472 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.