CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/21/16 15:48:53
| Available memory: 2.467 GB

INPUT: Reading input from 'pt-analysis.chi-py-py.in'
  [parm ../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apa]]
	Reading '../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apg]]
	Reading '../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpa]]
	Reading '../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpg]]
	Reading '../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apc]]
	Reading '../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apu]]
	Reading '../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpc]]
	Reading '../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpu]]
	Reading '../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpa]]
	Reading '../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpg]]
	Reading '../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upa]]
	Reading '../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upg]]
	Reading '../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpc]]
	Reading '../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpu]]
	Reading '../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upc]]
	Reading '../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [parm ../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upu]]
	Reading '../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [trajin ../../cc/cluster-all/km-5/ctraj.c3 parm [cpc]]
	Reading '../../cc/cluster-all/km-5/ctraj.c3' as Amber NetCDF
  [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c4 parm [cpu]]
	Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c4' as Amber NetCDF
  [trajin ../../uc/cluster-1-1/km-5/ctraj.c3 parm [upc]]
	Reading '../../uc/cluster-1-1/km-5/ctraj.c3' as Amber NetCDF
  [trajin ../../uu/cluster-all/km-5/ctraj.c2 parm [upu]]
	Reading '../../uu/cluster-all/km-5/ctraj.c2' as Amber NetCDF
  [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
    DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2]
              Output range is -180 to 180 degrees.
  [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
    DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2]
              Output range is -180 to 180 degrees.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (16 total):
 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (4 total):
 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544)
 1: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482)
 2: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047)
 3: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296)
  Coordinate processing will occur on 176369 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
  0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
  1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c3 (1-67544, 1) -----
 0% 10% 20% 30% 
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
  0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
  1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c4 (1-7482, 1) -----
40% 
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
  0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
  1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c3 (1-11047, 1) -----

.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
  0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
	 [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
  1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
	 [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c2 (1-90296, 1) -----
50% 60% 70% 80% 90% 100% Complete.

Read 176369 frames and processed 176369 frames.
TIME: Avg. throughput= 428436.7811 frames / second.

ACTION OUTPUT:

DATASETS (2 total):
	c1 "c1" (double, torsion(chin)), size is 176369
	c2 "c2" (double, torsion(chin)), size is 176369

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.02%)
TIME:		Trajectory Process : 0.4117 s ( 99.97%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.4118 s
---------- RUN END ---------------------------------------------------
  [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yy.gnu norm]
	Hist: 2dhist_c1_c2_yy.gnu: Set up for 2 dimensions using the following datasets:
	[ c1 c2 ]
	norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (16 total):
 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (4 total):
 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544)
 1: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482)
 2: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047)
 3: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296)
  Coordinate processing will occur on 176369 frames.

BEGIN TRAJECTORY PROCESSING:
----- ctraj.c3 (1-67544, 1) -----
 0% 10% 20% 30% 
----- ctraj.c4 (1-7482, 1) -----
40% 
----- ctraj.c3 (1-11047, 1) -----

----- ctraj.c2 (1-90296, 1) -----
50% 60% 70% 80% 90% 100% Complete.

Read 176369 frames and processed 176369 frames.
TIME: Avg. throughput= 561745.5393 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:
  0: [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yy.gnu norm]
		Calculating bins from min=-180 max=180 step=0.5.
	Dim c1: -180.000000->180.000000, step 0.500000, 720 bins.
		Calculating bins from min=-180 max=180 step=0.5.
	Dim c2: -180.000000->180.000000, step 0.500000, 720 bins.
	Hist: 176369 data points in each dimension.
	Hist: Allocating histogram, total bins = 518400
	Histogram: Normalizing sum of bin populations to 1.0
	           Sum over all bins is 176369

TIME: Analyses took 0.0113 seconds.

DATASETS (3 total):
	c1 "c1" (double, torsion(chin)), size is 176369
	c2 "c2" (double, torsion(chin)), size is 176369
	Hist_00018 "Hist_00018" (double matrix), size is 518400

DATAFILES (1 total):
  2dhist_c1_c2_yy.gnu (Gnuplot File):  Hist_00018

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.00%)
TIME:		Trajectory Process : 0.3140 s ( 26.86%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0113 s (  0.97%)
TIME:		Data File Write    : 0.8432 s ( 72.14%)
TIME:		Other              : 0.0003 s (  0.00%)
TIME:	Run Total 1.1688 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.6461 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.