CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 11/12/15 12:32:48
| Available memory: 3432.83 MB

INPUT: Reading Input from file pt-randomize.in
  [parm full.topo]
	Reading 'full.topo' as Amber Topology
	CHAMBER topology: 1:  CHARMM 361       *  \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ///
  [trajin non-randomized.crds]
	Reading 'non-randomized.crds' as Amber Restart
  [trajout rand.crds restart]
	Writing 'rand.crds' as Amber Restart
  [randomizeions :3-13 around :1-2 by 4.0 overlap 4.0 noimage seed 5]
    RANDOMIZEIONS: swapping the postions of the ions in mask [:3-13]
                   with the solvent. No ions can get closer than 4.00 angstroms
                   to another ion.
                   No ion can get closer than 4.00 angstroms to mask [:1-2]
                   Imaging of the coordinates will not be performed.
                   Random number generator seed is 5
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: full.topo, 3299 atoms, 1088 res, box: None, 1087 mol, 1075 solvent

INPUT TRAJECTORIES:
 0: 'non-randomized.crds' is an AMBER restart file, no velocities, Parm full.topo (reading 1 of 1)
  Coordinate processing will occur on 1 frames.

OUTPUT TRAJECTORIES:
  'rand.crds' (1 frames) is an AMBER restart file
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo' (1 actions):
  0: [randomizeions :3-13 around :1-2 by 4.0 overlap 4.0 noimage seed 5]
	Ion mask is [:3-13] (11 atoms)
	Around mask is [:1-2] (63 atoms)
----- non-randomized.crds (1-1, 1) -----
100% Complete.

Read 1 frames and processed 1 frames.
TIME: Trajectory processing: 0.0145 s
TIME: Avg. throughput= 68.7569 frames / second.

ACTION OUTPUT:

DATASETS:
  1 data set:
	full.topo "full.topo" (topology), size is 3299 full.topo, 3299 atoms, 1088 res, box: None, 1087 mol, 1075 solvent
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0541 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.