CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/30/15  11:22:34
| Available memory: 117102 MB

INPUT: Reading Input from file pt-kde-pca.in
  [parm ../../run1/build/full.topo.hmr [traj]]
	Reading '../../run1/build/full.topo.hmr' as Amber Topology
	CHAMBER topology: 1: CHARMM 361       *  \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ///
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [trajin ../../run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../run1/traj.1.02,../../run1/traj.1.03,../../run1/traj.1.04,../../run1/traj.1.05,../../run1/traj.1.06,../../run1/traj.1.07,../../run1/traj.1.08,../../run1/traj.1.09,../../run1/traj.1.10,../../run1/traj.1.11,../../run1/traj.1.12,../../run1/traj.1.13,../../run1/traj.1.14,../../run1/traj.1.15,../../run1/traj.1.16,../../run1/traj.1.17,../../run1/traj.1.18,]
  [trajin ../../run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../run2/traj.1.02,../../run2/traj.1.03,../../run2/traj.1.04,../../run2/traj.1.05,../../run2/traj.1.06,../../run2/traj.1.07,../../run2/traj.1.08,../../run2/traj.1.09,../../run2/traj.1.10,../../run2/traj.1.11,../../run2/traj.1.12,../../run2/traj.1.13,../../run2/traj.1.14,../../run2/traj.1.15,../../run2/traj.1.16,../../run2/traj.1.17,../../run2/traj.1.18,]
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
  [average avg.rst restart]
    AVERAGE: Averaging over coordinates in mask [*]
	Start: 1  Stop: Final frame
	Writing averaged coords to file 'avg.rst'
  [createcrd crd1]
    CREATECRD: Saving coordinates from Top [traj] to "crd1"
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [traj] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames

INPUT TRAJECTORIES:
 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
  Coordinate processing will occur on 100000 frames.
TIME: Run Initialization took 0.0124 seconds.

BEGIN TRAJECTORY PROCESSING:
	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[traj]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [rmsd :1,2&!@H= first]
	Target mask: [:1,2&!@H*](43)
	Reference mask: [:1,2&!@H*](43)
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.
  2: [average avg.rst restart]
	Averaging over 3303 atoms.
  3: [createcrd crd1]
Warning: COORDS data sets do not store temperatures.
Warning: COORDS data sets do not store times.
	Estimated memory usage (100000 frames): 3.8e+03 MB
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 100000 frames and processed 100000 frames.
TIME: Trajectory processing: 114.8381 s
TIME: Avg. throughput= 870.7911 frames / second.

ACTION OUTPUT:
    AVERAGE: [avg.rst restart]
	Writing 'avg.rst' as Amber Restart
  'avg.rst' is an AMBER restart file, Parm [traj]: Writing 1 frames (1-Last, 1)

DATASETS:
  2 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 100000
	crd1 "crd1" (coordinates), size is 100000 (3782.27 MB) Box Coords, 3303 atoms
---------- RUN END ---------------------------------------------------
  [reference avg.rst [avg]]
	Reading 'avg.rst' as Amber Restart
  [crdaction crd1 rms ref [avg] :1-2&!@H=]
	Using set 'crd1'
	Reference mask: [:1-2&!@H*](43)
    RMSD: (:1-2&!@H*), reference is "avg.rst" (:1-2&!@H*), with fitting.
	Target mask: [:1-2&!@H*](43)
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.
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 4.4774 seconds.
  [crdaction crd1 matrix covar :1-2&!@H= name DinucCovar]
	Using set 'crd1'
    MATRIX: Calculating covariance matrix, output is by atom.
	Matrix data set is 'DinucCovar'
	Start: 1  Stop: Final frame
	Mask1 is ':1-2&!@H*'
	Mask [:1-2&!@H*] corresponds to 43 atoms.
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 5.5249 seconds.
  [runanalysis diagmatrix DinucCovar out evecs.dat vecs 20]
	Changed DataFile 'evecs.dat' type to Evecs file for set Modes_00005
    DIAGMATRIX: Diagonalizing matrix DinucCovar and writing modes to evecs.dat
	Calculating 20 eigenvectors
TIME: Total analysis execution time: 0.1710 seconds.
  [crdaction crd1 projection T1 modes evecs.dat beg 1 end 10 :1-2&!@H= crdframes 1,50000 out T1.dat]
	Using set 'crd1'
	Reading modes from evecs.dat
	File contains 20 modes.
Warning: # modes to read (50) > modes in file. Only reading 20 modes.
    PROJECTION: Calculating projection using eigenvectors 1 to 10 of evecs.dat
	Results are written to T1.dat
	Start: 1  Stop: Final frame
	Atom Mask: [:1-2&!@H*]
	Mask [:1-2&!@H*] corresponds to 43 atoms.
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 2.6294 seconds.
  [crdaction crd1 projection T2 modes evecs.dat beg 1 end 10 :1-2&!@H= crdframes 50001,100000 out T2.dat]
	Using set 'crd1'
    PROJECTION: Calculating projection using eigenvectors 1 to 10 of evecs.dat
	Results are written to T2.dat
	Start: 1  Stop: Final frame
	Atom Mask: [:1-2&!@H*]
	Mask [:1-2&!@H*] corresponds to 43 atoms.
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 2.9851 seconds.
  [kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name TREMD-1]
    KDE: Using gaussian KDE to histogram set "Mode1"
	Calculating Kullback-Leibler divergence with set "Mode1"
	Bandwidth will be estimated.
  [kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name TREMD-2]
    KDE: Using gaussian KDE to histogram set "Mode2"
	Calculating Kullback-Leibler divergence with set "Mode2"
	Bandwidth will be estimated.
  [kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name TREMD-3]
    KDE: Using gaussian KDE to histogram set "Mode3"
	Calculating Kullback-Leibler divergence with set "Mode3"
	Bandwidth will be estimated.
  [kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name TREMD-4]
    KDE: Using gaussian KDE to histogram set "Mode4"
	Calculating Kullback-Leibler divergence with set "Mode4"
	Bandwidth will be estimated.
  [kde T1:5 kldiv T2:5 klout KL-PC.agr bins 400 name TREMD-5]
    KDE: Using gaussian KDE to histogram set "Mode5"
	Calculating Kullback-Leibler divergence with set "Mode5"
	Bandwidth will be estimated.
  [kde T1:6 kldiv T2:6 klout KL-PC.agr bins 400 name TREMD-6]
    KDE: Using gaussian KDE to histogram set "Mode6"
	Calculating Kullback-Leibler divergence with set "Mode6"
	Bandwidth will be estimated.
  [kde T1:7 kldiv T2:7 klout KL-PC.agr bins 400 name TREMD-7]
    KDE: Using gaussian KDE to histogram set "Mode7"
	Calculating Kullback-Leibler divergence with set "Mode7"
	Bandwidth will be estimated.
  [kde T1:8 kldiv T2:8 klout KL-PC.agr bins 400 name TREMD-8]
    KDE: Using gaussian KDE to histogram set "Mode8"
	Calculating Kullback-Leibler divergence with set "Mode8"
	Bandwidth will be estimated.
  [kde T1:9 kldiv T2:9 klout KL-PC.agr bins 400 name TREMD-9]
    KDE: Using gaussian KDE to histogram set "Mode9"
	Calculating Kullback-Leibler divergence with set "Mode9"
	Bandwidth will be estimated.
  [kde T1:10 kldiv T2:10 klout KL-PC.agr bins 400 name TREMD-10]
    KDE: Using gaussian KDE to histogram set "Mode10"
	Calculating Kullback-Leibler divergence with set "Mode10"
	Bandwidth will be estimated.
  [kde T1:1 out kde-PC.agr bins 400 name KDE1-1]
    KDE: Using gaussian KDE to histogram set "Mode1"
	Bandwidth will be estimated.
  [kde T2:1 out kde-PC.agr bins 400 name KDE1-2]
    KDE: Using gaussian KDE to histogram set "Mode1"
	Bandwidth will be estimated.
  [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode1 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T1:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN1]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode2 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T1:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN1]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode3 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T1:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN1]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode4 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T1:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN1]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode5 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T2:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN2]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode1 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T2:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN2]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode2 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T2:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN2]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode3 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T2:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN2]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode4 ]
	normint: Integral over bins will be normalized to 1.0.
  [hist T2:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN2]
	Hist: pca.hist.agr: Set up for 1 dimensions using the following datasets:
	[ Mode5 ]
	normint: Integral over bins will be normalized to 1.0.
  [run]
---------- RUN BEGIN -------------------------------------------------
Warning: No actions/output trajectories specified.

ANALYSIS: Performing 22 analyses:
  0: [kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name TREMD-1]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -10.753123->27.519667, step 0.095682, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.972489
	Parallelizing calculation with 24 threads
  1: [kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name TREMD-2]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -11.109071->19.018074, step 0.075318, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.856268
	Parallelizing calculation with 24 threads
  2: [kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name TREMD-3]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -12.249192->10.332132, step 0.056453, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.629026
	Parallelizing calculation with 24 threads
  3: [kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name TREMD-4]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -11.869795->10.711185, step 0.056452, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.474616
	Parallelizing calculation with 24 threads
  4: [kde T1:5 kldiv T2:5 klout KL-PC.agr bins 400 name TREMD-5]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -9.924988->11.466900, step 0.053480, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.427673
	Parallelizing calculation with 24 threads
  5: [kde T1:6 kldiv T2:6 klout KL-PC.agr bins 400 name TREMD-6]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -13.249703->10.955053, step 0.060512, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.346405
	Parallelizing calculation with 24 threads
Warning:	Kullback-Leibler divergence was undefined for 24 frames.
  6: [kde T1:7 kldiv T2:7 klout KL-PC.agr bins 400 name TREMD-7]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -10.392529->5.591202, step 0.039959, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.310494
	Parallelizing calculation with 24 threads
  7: [kde T1:8 kldiv T2:8 klout KL-PC.agr bins 400 name TREMD-8]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -8.026779->9.423594, step 0.043626, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.270374
	Parallelizing calculation with 24 threads
Warning:	Kullback-Leibler divergence was undefined for 4 frames.
  8: [kde T1:9 kldiv T2:9 klout KL-PC.agr bins 400 name TREMD-9]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -12.553227->7.402450, step 0.049889, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.249215
	Parallelizing calculation with 24 threads
Warning:	Kullback-Leibler divergence was undefined for 5 frames.
  9: [kde T1:10 kldiv T2:10 klout KL-PC.agr bins 400 name TREMD-10]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -7.710034->7.810487, step 0.038801, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.201776
	Parallelizing calculation with 24 threads
Warning:	Kullback-Leibler divergence was undefined for 5 frames.
  10: [kde T1:1 out kde-PC.agr bins 400 name KDE1-1]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -10.983047->27.519667, step 0.096257, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.972489
	Parallelizing calculation with 24 threads
  11: [kde T2:1 out kde-PC.agr bins 400 name KDE1-2]
	No minimum specified, determining from input data.
	No maximum specified, determining from input data.
	Dim : -10.753123->28.886993, step 0.099100, 400 bins.
	Determined bandwidth from normal distribution approximation: 0.957210
	Parallelizing calculation with 24 threads
  12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1]
	Dim T1:1: -10.983047->27.519667, step 0.192514, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 47345 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  13: [hist T1:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN1]
	Dim T1:2: -11.109071->19.018074, step 0.150636, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 48955 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  14: [hist T1:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN1]
	Dim T1:3: -12.249192->10.375493, step 0.113123, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 35700 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  15: [hist T1:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN1]
	Dim T1:4: -12.493841->10.711185, step 0.116025, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 43861 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  16: [hist T1:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN1]
	Dim T1:5: -9.950069->11.466900, step 0.107085, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 49631 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  17: [hist T2:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN2]
	Dim T2:1: -10.753123->28.886993, step 0.198201, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 28097 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  18: [hist T2:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN2]
	Dim T2:2: -11.283357->19.391811, step 0.153376, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 41159 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  19: [hist T2:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN2]
	Dim T2:3: -12.288095->10.332132, step 0.113101, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 21286 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  20: [hist T2:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN2]
	Dim T2:4: -11.869795->10.754849, step 0.113123, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 5913 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000
  21: [hist T2:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN2]
	Dim T2:5: -9.924988->11.614499, step 0.107697, 200 bins.
	Hist: 50000 data points in each dimension.
	Hist: Allocating histogram, total bins = 200
	Warning: Frame 12067 Coordinates out of bounds (200)
	Histogram: Normalizing integral over bin populations to 1.0
	           Sum over all bins is 49999.000000

TIME: Analyses took 10.9532 seconds.

DATASETS:
  59 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 100000
	crd1 "crd1" (coordinates), size is 100000 (3782.27 MB) Box Coords, 3303 atoms
	[avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst', refindex 0 (3303 atoms)
	RMSD_00003 "RMSD_00003" (double, rms), size is 100000
	DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 8385
	Modes_00005 "Modes_00005" (eigenmodes(covariance)), size is 20
	evecs.dat "evecs.dat" (eigenmodes(covariance)), size is 20
	T1:1 "Mode1" (float), size is 50000
	T1:2 "Mode2" (float), size is 50000
	T1:3 "Mode3" (float), size is 50000
	T1:4 "Mode4" (float), size is 50000
	T1:5 "Mode5" (float), size is 50000
	T1:6 "Mode6" (float), size is 50000
	T1:7 "Mode7" (float), size is 50000
	T1:8 "Mode8" (float), size is 50000
	T1:9 "Mode9" (float), size is 50000
	T1:10 "Mode10" (float), size is 50000
	T2:1 "Mode1" (float), size is 50000
	T2:2 "Mode2" (float), size is 50000
	T2:3 "Mode3" (float), size is 50000
	T2:4 "Mode4" (float), size is 50000
	T2:5 "Mode5" (float), size is 50000
	T2:6 "Mode6" (float), size is 50000
	T2:7 "Mode7" (float), size is 50000
	T2:8 "Mode8" (float), size is 50000
	T2:9 "Mode9" (float), size is 50000
	T2:10 "Mode10" (float), size is 50000
	TREMD-1 "TREMD-1" (double), size is 400
	TREMD-1[kld] "TREMD-1[kld]" (double), size is 50000
	TREMD-2 "TREMD-2" (double), size is 400
	TREMD-2[kld] "TREMD-2[kld]" (double), size is 50000
	TREMD-3 "TREMD-3" (double), size is 400
	TREMD-3[kld] "TREMD-3[kld]" (double), size is 50000
	TREMD-4 "TREMD-4" (double), size is 400
	TREMD-4[kld] "TREMD-4[kld]" (double), size is 50000
	TREMD-5 "TREMD-5" (double), size is 400
	TREMD-5[kld] "TREMD-5[kld]" (double), size is 50000
	TREMD-6 "TREMD-6" (double), size is 400
	TREMD-6[kld] "TREMD-6[kld]" (double), size is 50000
	TREMD-7 "TREMD-7" (double), size is 400
	TREMD-7[kld] "TREMD-7[kld]" (double), size is 50000
	TREMD-8 "TREMD-8" (double), size is 400
	TREMD-8[kld] "TREMD-8[kld]" (double), size is 50000
	TREMD-9 "TREMD-9" (double), size is 400
	TREMD-9[kld] "TREMD-9[kld]" (double), size is 50000
	TREMD-10 "TREMD-10" (double), size is 400
	TREMD-10[kld] "TREMD-10[kld]" (double), size is 50000
	KDE1-1 "KDE1-1" (double), size is 400
	KDE1-2 "KDE1-2" (double), size is 400
	PC1-RUN1 "PC1-RUN1" (double), size is 200
	PC2-RUN1 "PC2-RUN1" (double), size is 200
	PC3-RUN1 "PC3-RUN1" (double), size is 200
	PC4-RUN1 "PC4-RUN1" (double), size is 200
	PC5-RUN1 "PC5-RUN1" (double), size is 200
	PC1-RUN2 "PC1-RUN2" (double), size is 200
	PC2-RUN2 "PC2-RUN2" (double), size is 200
	PC3-RUN2 "PC3-RUN2" (double), size is 200
	PC4-RUN2 "PC4-RUN2" (double), size is 200
	PC5-RUN2 "PC5-RUN2" (double), size is 200

DATAFILES:
  evecs.dat (Evecs file):  Modes_00005
  T1.dat (Standard Data File):  Mode1 Mode2 Mode3 Mode4 Mode5 Mode6 Mode7 Mode8 Mode9 Mode10
  T2.dat (Standard Data File):  Mode1 Mode2 Mode3 Mode4 Mode5 Mode6 Mode7 Mode8 Mode9 Mode10
  KL-PC.agr (Grace File):  TREMD-1[kld] TREMD-2[kld] TREMD-3[kld] TREMD-4[kld] TREMD-5[kld] TREMD-6[kld] TREMD-7[kld] TREMD-8[kld] TREMD-9[kld] TREMD-10[kld]
  kde-PC.agr (Grace File):  KDE1-1 KDE1-2
  pca.hist.agr (Grace File):  PC1-RUN1 PC2-RUN1 PC3-RUN1 PC4-RUN1 PC5-RUN1 PC1-RUN2 PC2-RUN2 PC3-RUN2 PC4-RUN2 PC5-RUN2
---------- RUN END ---------------------------------------------------
  [modes eigenval name evecs.dat out modes-fraction.dat]
    ANALYZE MODES: Calculating eigenvalue fraction using modes from evecs.dat
	Results are written to modes-fraction.dat
---------- RUN BEGIN -------------------------------------------------
Warning: No actions/output trajectories specified.

ANALYSIS: Performing 1 analyses:
  0: [modes eigenval name evecs.dat out modes-fraction.dat]
	20 eigenvalues, sum is 202.167230

TIME: Analyses took 0.0021 seconds.

DATASETS:
  59 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 100000
	crd1 "crd1" (coordinates), size is 100000 (3782.27 MB) Box Coords, 3303 atoms
	[avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst', refindex 0 (3303 atoms)
	RMSD_00003 "RMSD_00003" (double, rms), size is 100000
	DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 8385
	Modes_00005 "Modes_00005" (eigenmodes(covariance)), size is 20
	evecs.dat "evecs.dat" (eigenmodes(covariance)), size is 20
	T1:1 "Mode1" (float), size is 50000
	T1:2 "Mode2" (float), size is 50000
	T1:3 "Mode3" (float), size is 50000
	T1:4 "Mode4" (float), size is 50000
	T1:5 "Mode5" (float), size is 50000
	T1:6 "Mode6" (float), size is 50000
	T1:7 "Mode7" (float), size is 50000
	T1:8 "Mode8" (float), size is 50000
	T1:9 "Mode9" (float), size is 50000
	T1:10 "Mode10" (float), size is 50000
	T2:1 "Mode1" (float), size is 50000
	T2:2 "Mode2" (float), size is 50000
	T2:3 "Mode3" (float), size is 50000
	T2:4 "Mode4" (float), size is 50000
	T2:5 "Mode5" (float), size is 50000
	T2:6 "Mode6" (float), size is 50000
	T2:7 "Mode7" (float), size is 50000
	T2:8 "Mode8" (float), size is 50000
	T2:9 "Mode9" (float), size is 50000
	T2:10 "Mode10" (float), size is 50000
	TREMD-1 "TREMD-1" (double), size is 400
	TREMD-1[kld] "TREMD-1[kld]" (double), size is 50000
	TREMD-2 "TREMD-2" (double), size is 400
	TREMD-2[kld] "TREMD-2[kld]" (double), size is 50000
	TREMD-3 "TREMD-3" (double), size is 400
	TREMD-3[kld] "TREMD-3[kld]" (double), size is 50000
	TREMD-4 "TREMD-4" (double), size is 400
	TREMD-4[kld] "TREMD-4[kld]" (double), size is 50000
	TREMD-5 "TREMD-5" (double), size is 400
	TREMD-5[kld] "TREMD-5[kld]" (double), size is 50000
	TREMD-6 "TREMD-6" (double), size is 400
	TREMD-6[kld] "TREMD-6[kld]" (double), size is 50000
	TREMD-7 "TREMD-7" (double), size is 400
	TREMD-7[kld] "TREMD-7[kld]" (double), size is 50000
	TREMD-8 "TREMD-8" (double), size is 400
	TREMD-8[kld] "TREMD-8[kld]" (double), size is 50000
	TREMD-9 "TREMD-9" (double), size is 400
	TREMD-9[kld] "TREMD-9[kld]" (double), size is 50000
	TREMD-10 "TREMD-10" (double), size is 400
	TREMD-10[kld] "TREMD-10[kld]" (double), size is 50000
	KDE1-1 "KDE1-1" (double), size is 400
	KDE1-2 "KDE1-2" (double), size is 400
	PC1-RUN1 "PC1-RUN1" (double), size is 200
	PC2-RUN1 "PC2-RUN1" (double), size is 200
	PC3-RUN1 "PC3-RUN1" (double), size is 200
	PC4-RUN1 "PC4-RUN1" (double), size is 200
	PC5-RUN1 "PC5-RUN1" (double), size is 200
	PC1-RUN2 "PC1-RUN2" (double), size is 200
	PC2-RUN2 "PC2-RUN2" (double), size is 200
	PC3-RUN2 "PC3-RUN2" (double), size is 200
	PC4-RUN2 "PC4-RUN2" (double), size is 200
	PC5-RUN2 "PC5-RUN2" (double), size is 200

DATAFILES:
  evecs.dat (Evecs file):  Modes_00005
  T1.dat (Standard Data File):  Mode1 Mode2 Mode3 Mode4 Mode5 Mode6 Mode7 Mode8 Mode9 Mode10
  T2.dat (Standard Data File):  Mode1 Mode2 Mode3 Mode4 Mode5 Mode6 Mode7 Mode8 Mode9 Mode10
  KL-PC.agr (Grace File):  TREMD-1[kld] TREMD-2[kld] TREMD-3[kld] TREMD-4[kld] TREMD-5[kld] TREMD-6[kld] TREMD-7[kld] TREMD-8[kld] TREMD-9[kld] TREMD-10[kld]
  kde-PC.agr (Grace File):  KDE1-1 KDE1-2
  pca.hist.agr (Grace File):  PC1-RUN1 PC2-RUN1 PC3-RUN1 PC4-RUN1 PC5-RUN1 PC1-RUN2 PC2-RUN2 PC3-RUN2 PC4-RUN2 PC5-RUN2
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 145.3651 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.