CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/24/15 12:08:50
| Available memory: 121471 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
[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,]
Warning: RemdTraj: Replica ../../run2/traj.1.08 frames (48446) does not match
Warning: # frames in first replica (48447).
Warning: RemdTraj: Setting total # of frames to 48446
Warning: RemdTraj: Replica ../../run2/traj.1.10 frames (48447) does not match
Warning: # frames in first replica (48446).
Warning: RemdTraj: Replica ../../run2/traj.1.11 frames (48447) does not match
Warning: # frames in first replica (48446).
Warning: RemdTraj: Replica ../../run2/traj.1.12 frames (48447) does not match
Warning: # frames in first replica (48446).
Warning: RemdTraj: Replica ../../run2/traj.1.14 frames (48447) does not match
Warning: # frames in first replica (48446).
Warning: RemdTraj: Replica ../../run2/traj.1.15 frames (48447) does not match
Warning: # frames in first replica (48446).
Warning: RemdTraj: Replica ../../run2/traj.1.16 frames (48447) does not match
Warning: # frames in first replica (48446).
[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', 4370 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 98127 frames
INPUT TRAJECTORIES:
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49681 of 49681)
Looking for frames at 298.41 K
1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 48446 of 48446)
Looking for frames at 298.41 K
Coordinate processing will occur on 98127 frames.
TIME: Run Initialization took 0.0120 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*](37)
Reference 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.
2: [average avg.rst restart]
Averaging over 4370 atoms.
3: [createcrd crd1]
Warning: COORDS data sets do not store temperatures.
Warning: COORDS data sets do not store times.
Estimated memory usage (98127 frames): 4.9e+03 MB
----- traj.1.01 (1-49681, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-48446, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 98127 frames and processed 98127 frames.
TIME: Trajectory processing: 186.4216 s
TIME: Avg. throughput= 526.3715 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 98127
crd1 "crd1" (coordinates), size is 98127 (4909.64 MB) Box Coords, 4370 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*](37)
RMSD: (:1-2&!@H*), reference is "avg.rst" (:1-2&!@H*), with fitting.
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.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 5.6239 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 37 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 6.2889 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: 0.0421 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 37 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 3.3626 seconds.
[crdaction crd1 projection T2 modes evecs.dat beg 1 end 10 :1-2&!@H= crdframes 50001,100000 out T2.dat]
Using set 'crd1'
Warning: stop 100000 > #Frames (98127), setting to max.
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 37 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 3.7609 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 : -9.710149->22.567102, step 0.080693, 400 bins.
Determined bandwidth from normal distribution approximation: 0.964154
Parallelizing calculation with 24 threads
Warning: Size of Mode1 (50000) != size of Mode1 (48127)
Warning: Only using 48127 data points.
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 : -16.326296->11.797709, step 0.070310, 400 bins.
Determined bandwidth from normal distribution approximation: 0.562110
Parallelizing calculation with 24 threads
Warning: Size of Mode2 (50000) != size of Mode2 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 25 frames.
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 : -12.926908->11.176179, step 0.060258, 400 bins.
Determined bandwidth from normal distribution approximation: 0.493736
Parallelizing calculation with 24 threads
Warning: Size of Mode3 (50000) != size of Mode3 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 2 frames.
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 : -15.455733->7.857928, step 0.058284, 400 bins.
Determined bandwidth from normal distribution approximation: 0.337566
Parallelizing calculation with 24 threads
Warning: Size of Mode4 (50000) != size of Mode4 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 4 frames.
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 : -11.442052->11.803973, step 0.058115, 400 bins.
Determined bandwidth from normal distribution approximation: 0.322703
Parallelizing calculation with 24 threads
Warning: Size of Mode5 (50000) != size of Mode5 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 3 frames.
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 : -9.180564->7.417319, step 0.041495, 400 bins.
Determined bandwidth from normal distribution approximation: 0.203954
Parallelizing calculation with 24 threads
Warning: Size of Mode6 (50000) != size of Mode6 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 5 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 : -7.164962->8.292514, step 0.038644, 400 bins.
Determined bandwidth from normal distribution approximation: 0.174172
Parallelizing calculation with 24 threads
Warning: Size of Mode7 (50000) != size of Mode7 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 81 frames.
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 : -7.040624->5.227742, step 0.030671, 400 bins.
Determined bandwidth from normal distribution approximation: 0.158574
Parallelizing calculation with 24 threads
Warning: Size of Mode8 (50000) != size of Mode8 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 32 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 : -6.342803->6.259595, step 0.031506, 400 bins.
Determined bandwidth from normal distribution approximation: 0.153652
Parallelizing calculation with 24 threads
Warning: Size of Mode9 (50000) != size of Mode9 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 10 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 : -5.694357->6.227877, step 0.029806, 400 bins.
Determined bandwidth from normal distribution approximation: 0.147669
Parallelizing calculation with 24 threads
Warning: Size of Mode10 (50000) != size of Mode10 (48127)
Warning: Only using 48127 data points.
Warning: Kullback-Leibler divergence was undefined for 4 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 : -9.710149->22.827606, step 0.081344, 400 bins.
Determined bandwidth from normal distribution approximation: 0.964154
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 : -9.787197->22.567102, step 0.080886, 400 bins.
Determined bandwidth from normal distribution approximation: 0.994512
Parallelizing calculation with 24 threads
12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1]
Dim T1:1: -9.710149->22.827606, step 0.162689, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 50000.000000
13: [hist T1:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN1]
Dim T1:2: -16.371315->11.797709, step 0.140845, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 39174 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: -13.118354->11.446625, step 0.122825, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 18806 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: -15.455733->7.907028, step 0.116814, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 20047 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: -11.442052->11.803973, step 0.116230, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 15453 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: -9.787197->22.567102, step 0.161771, 200 bins.
Hist: 48127 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 45113 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 48126.000000
18: [hist T2:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN2]
Dim T2:2: -16.326296->12.218953, step 0.142726, 200 bins.
Hist: 48127 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 24755 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 48126.000000
19: [hist T2:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN2]
Dim T2:3: -12.926908->11.176179, step 0.120515, 200 bins.
Hist: 48127 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 26496 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 48126.000000
20: [hist T2:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN2]
Dim T2:4: -15.605559->7.857928, step 0.117317, 200 bins.
Hist: 48127 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 22650 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 48126.000000
21: [hist T2:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN2]
Dim T2:5: -11.709357->12.174574, step 0.119420, 200 bins.
Hist: 48127 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 10900 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 48126.000000
TIME: Analyses took 11.4180 seconds.
DATASETS:
59 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 98127
crd1 "crd1" (coordinates), size is 98127 (4909.64 MB) Box Coords, 4370 atoms
[avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst', refindex 0 (4370 atoms)
RMSD_00003 "RMSD_00003" (double, rms), size is 98127
DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 6216
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 48127
T2:2 "Mode2" (float), size is 48127
T2:3 "Mode3" (float), size is 48127
T2:4 "Mode4" (float), size is 48127
T2:5 "Mode5" (float), size is 48127
T2:6 "Mode6" (float), size is 48127
T2:7 "Mode7" (float), size is 48127
T2:8 "Mode8" (float), size is 48127
T2:9 "Mode9" (float), size is 48127
T2:10 "Mode10" (float), size is 48127
TREMD-1 "TREMD-1" (double), size is 400
TREMD-1[kld] "TREMD-1[kld]" (double), size is 48127
TREMD-2 "TREMD-2" (double), size is 400
TREMD-2[kld] "TREMD-2[kld]" (double), size is 48127
TREMD-3 "TREMD-3" (double), size is 400
TREMD-3[kld] "TREMD-3[kld]" (double), size is 48127
TREMD-4 "TREMD-4" (double), size is 400
TREMD-4[kld] "TREMD-4[kld]" (double), size is 48127
TREMD-5 "TREMD-5" (double), size is 400
TREMD-5[kld] "TREMD-5[kld]" (double), size is 48127
TREMD-6 "TREMD-6" (double), size is 400
TREMD-6[kld] "TREMD-6[kld]" (double), size is 48127
TREMD-7 "TREMD-7" (double), size is 400
TREMD-7[kld] "TREMD-7[kld]" (double), size is 48127
TREMD-8 "TREMD-8" (double), size is 400
TREMD-8[kld] "TREMD-8[kld]" (double), size is 48127
TREMD-9 "TREMD-9" (double), size is 400
TREMD-9[kld] "TREMD-9[kld]" (double), size is 48127
TREMD-10 "TREMD-10" (double), size is 400
TREMD-10[kld] "TREMD-10[kld]" (double), size is 48127
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 133.263080
TIME: Analyses took 0.0308 seconds.
DATASETS:
59 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 98127
crd1 "crd1" (coordinates), size is 98127 (4909.64 MB) Box Coords, 4370 atoms
[avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst', refindex 0 (4370 atoms)
RMSD_00003 "RMSD_00003" (double, rms), size is 98127
DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 6216
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 48127
T2:2 "Mode2" (float), size is 48127
T2:3 "Mode3" (float), size is 48127
T2:4 "Mode4" (float), size is 48127
T2:5 "Mode5" (float), size is 48127
T2:6 "Mode6" (float), size is 48127
T2:7 "Mode7" (float), size is 48127
T2:8 "Mode8" (float), size is 48127
T2:9 "Mode9" (float), size is 48127
T2:10 "Mode10" (float), size is 48127
TREMD-1 "TREMD-1" (double), size is 400
TREMD-1[kld] "TREMD-1[kld]" (double), size is 48127
TREMD-2 "TREMD-2" (double), size is 400
TREMD-2[kld] "TREMD-2[kld]" (double), size is 48127
TREMD-3 "TREMD-3" (double), size is 400
TREMD-3[kld] "TREMD-3[kld]" (double), size is 48127
TREMD-4 "TREMD-4" (double), size is 400
TREMD-4[kld] "TREMD-4[kld]" (double), size is 48127
TREMD-5 "TREMD-5" (double), size is 400
TREMD-5[kld] "TREMD-5[kld]" (double), size is 48127
TREMD-6 "TREMD-6" (double), size is 400
TREMD-6[kld] "TREMD-6[kld]" (double), size is 48127
TREMD-7 "TREMD-7" (double), size is 400
TREMD-7[kld] "TREMD-7[kld]" (double), size is 48127
TREMD-8 "TREMD-8" (double), size is 400
TREMD-8[kld] "TREMD-8[kld]" (double), size is 48127
TREMD-9 "TREMD-9" (double), size is 400
TREMD-9[kld] "TREMD-9[kld]" (double), size is 48127
TREMD-10 "TREMD-10" (double), size is 400
TREMD-10[kld] "TREMD-10[kld]" (double), size is 48127
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: 220.9716 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.