CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 04/18/16 12:27:08
| Available memory: 1.536 GB

INPUT: Reading input from 'pt-rmsd.in'
  [parm ../../build/full.topo.hmr [traj]]
	Reading '../../build/full.topo.hmr' as Amber Topology
  [parm ../../../../../A-form.pdb [striped]]
	Reading '../../../../../A-form.pdb' as PDB File
	Determining bond info from distances.
Warning: A-form.pdb: Determining default bond distances from element types.
  [reference ../../../../../A-form.pdb parm [striped] [a-form]]
	Reading '../../../../../A-form.pdb' as PDB
	Setting active reference for distance-based masks: 'A-form.pdb'
Warning: Active reference has only 65 atoms, parm 'full.topo.hmr' has 3301.
Warning: Parm will only have reference coordinates for the first 65 atoms (distance-based masks only).
  [strip :WAT,Na+,K+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
    STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-]
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [rmsd rms_2_aform :1,2&!@H= out rmsd_18.dat ref [a-form]]
    RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*).
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [trajin ../../traj.1.18]
	Reading '../../traj.1.18' as Amber NetCDF
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (2 total):
 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
 1: [striped] A-form.pdb, 65 atoms, 2 res, box: None, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'traj.1.18' is a NetCDF AMBER trajectory with replica temperatures, Parm full.topo.hmr (Orthogonal box) (reading 50000 of 50000)
  Coordinate processing will occur on 50000 frames.

REFERENCE FRAMES (1 total):
    0: [a-form]:1
	Active reference frame for distance-based masks is '[a-form]:1'

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (3 actions):
  0: [strip :WAT,Na+,K+,Cl-]
	Stripping 3236 atoms.
	Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [rmsd rms_2_aform :1,2&!@H= out rmsd_18.dat ref [a-form]]
	Target mask: [:1,2&!@H*](41)
	Reference mask: [:1,2&!@H*](41)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
----- traj.1.18 (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= 171.8834 frames / second.

ACTION OUTPUT:

DATASETS (1 total):
	rms_2_aform "rms_2_aform" (double, rms), size is 50000

DATAFILES (1 total):
  rmsd_18.dat (Standard Data File):  rms_2_aform

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.00%)
TIME:		Trajectory Process : 290.8949 s ( 91.58%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 26.7358 s (  8.42%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 317.6308 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 328.2883 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.