CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/12/15  10:52:37
| Available memory: 83653.3 MB

INPUT: Reading Input from file 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
	A-form.pdb: 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
  [strip :WAT,Na+,K+,Cl-]
    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]]
	Reference mask: [:1,2&!@H*](37)
    RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting.
  [trajin ../../traj.1.18 ]
	Reading '../../traj.1.18' as Amber NetCDF
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [traj] 'full.topo.hmr', 3295 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames
 1: [striped] 'A-form.pdb', 59 atoms, 2 res, box: None, 1 mol

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

REFERENCE FRAMES (1 total):
    0: '../../../../../A-form.pdb', frame 1
	Active reference frame for distance-based masks is 0
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
Warning: Active reference has only 59 atoms, parm '[traj]' has 3295.
Warning: Parm will only have reference coordinates for the first 59 atoms (distance-based masks only).
.....................................................
ACTION SETUP FOR PARM '[traj]' (3 actions):
  0: [strip :WAT,Na+,K+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 59 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*](37)
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: Trajectory processing: 4.9592 s
TIME: Avg. throughput= 10082.3140 frames / second.

ACTION OUTPUT:

DATASETS:
  2 data sets:
	[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../A-form.pdb', refindex 0 (59 atoms)
	rms_2_aform "rms_2_aform" (double, rms), size is 50000

DATAFILES:
  rmsd_18.dat (Standard Data File):  rms_2_aform
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 5.3104 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.