CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 09/09/16  12:42:00
| Available memory: 505.742 MB

	Reading '3erd_wat.prmtop' as Amber Topology
INPUT: Reading Input from file rmsd.in
  [trajin 3erd_wat_md1.crd]
	Reading '3erd_wat_md1.crd' as Amber Trajectory
  [trajin 3erd_wat_md2.crd]
	Reading '3erd_wat_md2.crd' as Amber Trajectory
  [trajin 3erd_wat_md3.crd]
	Reading '3erd_wat_md3.crd' as Amber Trajectory
  [strip :WAT]
    STRIP: Stripping atoms in mask [:WAT]
  [strip :Na+]
    STRIP: Stripping atoms in mask [:Na+]
  [autoimage]
    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
  [rms first out try1-rmsd.dat :1-246@CA]
    RMSD: (:1-246@CA), reference is first frame (:1-246@CA), with fitting.
  [atomicfluct out try1-Per-res-fluct.dat :1-246 byres]
    ATOMICFLUCT: calculating atomic positional fluctuations, output to file try1-Per-res-fluct.dat
                 Atom mask: [:1-246]
	Start: 1  Stop: Final frame
  [atomicfluct out try1-CA-fluct.dat @CA byatom]
    ATOMICFLUCT: calculating atomic positional fluctuations, output to file try1-CA-fluct.dat
                 Atom mask: [@CA]
	Start: 1  Stop: Final frame
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: '3erd_wat.prmtop', 36725 atoms, 11162 res, box: Orthogonal, 10917 mol, 10910 solvent, 10100 frames

INPUT TRAJECTORIES:
 0: '3erd_wat_md1.crd' is an AMBER trajectory, Parm 3erd_wat.prmtop (Orthogonal box) (reading 100 of 100)
 1: '3erd_wat_md2.crd' is an AMBER trajectory, Parm 3erd_wat.prmtop (Orthogonal box) (reading 5000 of 5000)
 2: '3erd_wat_md3.crd' is an AMBER trajectory, Parm 3erd_wat.prmtop (Orthogonal box) (reading 5000 of 5000)
  Coordinate processing will occur on 10100 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '3erd_wat.prmtop' (6 actions):
  0: [strip :WAT]
	Stripping 32730 atoms.
	Stripped parm: '3erd_wat.prmtop', 3995 atoms, 252 res, box: Orthogonal, 7 mol
  1: [strip :Na+]
	Stripping 6 atoms.
	Stripped parm: '3erd_wat.prmtop', 3989 atoms, 246 res, box: Orthogonal, 1 mol
  2: [autoimage]
	Anchor molecule is 1
	0 molecules are mobile.
  3: [rms first out try1-rmsd.dat :1-246@CA]
	Target mask: [:1-246@CA](246)
	Reference mask: [:1-246@CA](246)
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.
  4: [atomicfluct out try1-Per-res-fluct.dat :1-246 byres]
	Mask [:1-246] corresponds to 3989 atoms.
  5: [atomicfluct out try1-CA-fluct.dat @CA byatom]
	Mask [@CA] corresponds to 246 atoms.
----- 3erd_wat_md1.crd (1-100, 1) -----
 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete.

----- 3erd_wat_md2.crd (1-5000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

----- 3erd_wat_md3.crd (1-5000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 10100 frames and processed 10100 frames.
TIME: Trajectory processing: 208.8676 s
TIME: Avg. throughput= 48.3560 frames / second.

ACTION OUTPUT:
    ATOMICFLUCT: Calculating fluctuations for 10100 sets.
    ATOMICFLUCT: Calculating fluctuations for 10100 sets.

DATASETS:
  3 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 10100
	Fluct_00001 "AtomicFlx" (X-Y mesh), size is 246
	Fluct_00002 "AtomicFlx" (X-Y mesh), size is 246

DATAFILES:
  try1-rmsd.dat (Standard Data File):  RMSD_00000
  try1-Per-res-fluct.dat (Standard Data File):  AtomicFlx
  try1-CA-fluct.dat (Standard Data File):  AtomicFlx
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 209.1105 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.