CPPTRAJ: Trajectory Analysis. V15.00
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 10/29/15  09:17:09
| Available memory: 2609.95 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.
  [trajin ../traj.1.16 ]
	Reading '../traj.1.16' as Amber NetCDF
  [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= ref [a-form]]
	Reference mask: [:1,2&!@H*](39)
    RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [traj] 'full.topo.hmr', 3730 atoms, 927 res, box: Orthogonal, 926 mol, 914 solvent, 50000 frames
 1: [striped] 'A-form.pdb', 63 atoms, 2 res, box: None, 1 mol

INPUT TRAJECTORIES:
 0: 'traj.1.16' 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 63 atoms, parm '[traj]' has 3730.
Warning: Parm will only have reference coordinates for the first 63 atoms (distance-based masks only).
.....................................................
ACTION SETUP FOR PARM '[traj]' (3 actions):
  0: [strip :WAT,Na+,K+,Cl-]
	Stripping 3667 atoms.
	Stripped parm: 'full.topo.hmr', 63 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= ref [a-form]]
	Target mask: [:1,2&!@H*](39)
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.1.16 (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: 4.6317 s
TIME: Avg. throughput= 10795.0745 frames / second.

ACTION OUTPUT:

DATASETS:
  2 data sets:
	[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb', refindex 0 (63 atoms)
	rms_2_aform "rms_2_aform" (double, rms), size is 50000
---------- RUN END ---------------------------------------------------
  [hist rms_2_aform,0,5,0.1 out hist_rmsd_16.dat norm]
	Hist: hist_rmsd_16.dat: Set up for 1 dimensions using the following datasets:
	[ rms_2_aform ]
	norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------
Warning: No actions/output trajectories specified.

ANALYSIS: Performing 1 analyses:
  0: [hist rms_2_aform,0,5,0.1 out hist_rmsd_16.dat norm]
	Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 50
	Warning: Frame 6960 Coordinates out of bounds (-1)
	Warning: Frame 10516 Coordinates out of bounds (-1)
	Warning: Frame 10526 Coordinates out of bounds (-1)
	Warning: Frame 10529 Coordinates out of bounds (-1)
	Warning: Frame 24263 Coordinates out of bounds (-1)
	Warning: Frame 27831 Coordinates out of bounds (-1)
	Warning: Frame 36321 Coordinates out of bounds (-1)
	Warning: Frame 36498 Coordinates out of bounds (-1)
	Warning: Frame 36499 Coordinates out of bounds (-1)
	Warning: Frame 40694 Coordinates out of bounds (-1)
	Warning: Frame 48286 Coordinates out of bounds (-1)
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 49989.000000

TIME: Analyses took 0.0004 seconds.

DATASETS:
  3 data sets:
	[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb', refindex 0 (63 atoms)
	rms_2_aform "rms_2_aform" (double, rms), size is 50000
	Hist_00002 "Hist_00002" (double), size is 50

DATAFILES:
  hist_rmsd_16.dat (Standard Data File):  Hist_00002
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 4.7312 seconds.
--------------------------------------------------------------------------------
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.