CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/03/16 09:56:51
| Available memory: 4.953 GB

INPUT: Reading input from '../../../../../scripts/pt-randomize.in'
  [parm full.topo]
	Reading 'full.topo' as Amber Topology
  [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 3]
    RANDOMIZEIONS: Swapping postions of ions in mask ':3-13' with solvent.
	No ion can get closer than 4.00 angstroms to another ion.
	No ion can get closer than 4.00 angstroms to atoms in mask ':1-2'
	Imaging of the coordinates will not be performed.
	Random number generator seed is 3
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: full.topo, 3302 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent

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

OUTPUT TRAJECTORIES (1 total):
  'rand.crds' (1 frames) is an AMBER restart file

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 3]
	Ion mask is ':3-13' (11 atoms)
	Around mask is ':1-2' (66 atoms)
----- non-randomized.crds (1-1, 1) -----
100% Complete.

Read 1 frames and processed 1 frames.
TIME: Avg. throughput= 63.3633 frames / second.

ACTION OUTPUT:

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.13%)
TIME:		Trajectory Process : 0.0158 s ( 99.40%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 0.0159 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0431 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.