CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/08/16 09:05:58
| Available memory: 16.007 GB
INPUT: Reading input from 'pt-kde-pca.in'
[parm ../../run1/build/full.topo.hmr [traj]]
Reading '../../run1/build/full.topo.hmr' as Amber Topology
[autoimage origin]
Warning: Action specified before trajin/ensemble. Assuming trajin.
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,]
Reading '../../run1/traj.1.01' as Amber NetCDF
[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,]
Reading '../../run2/traj.1.01' as Amber NetCDF
[rmsd :1,2&!@H= first]
RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
[average avg.rst restart]
Writing 'avg.rst' as Amber 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 full.topo.hmr to "crd1"
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (2 total):
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.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [rmsd :1,2&!@H= first]
Target mask: [:1,2&!@H*](40)
Reference mask: [:1,2&!@H*](40)
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]
Mask [*] corresponds to 3299 atoms.
Averaging over 3299 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): 3.961 GB
----- traj.1.01 (1-50000, 1) -----
0% 10% 20% 30% 40%
----- traj.1.01 (1-50000, 1) -----
50% 60% 70% 80% 90% 100% Complete.
Read 100000 frames and processed 100000 frames.
TIME: Avg. throughput= 58.9804 frames / second.
ACTION OUTPUT:
AVERAGE: 100000 frames, 'avg.rst' is an AMBER restart file, Parm full.topo.hmr: Writing 1 frames (1-Last, 1)
DATASETS (2 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
crd1 "crd1" (coordinates), size is 100000 (3.961 GB) Box Coords, 3299 atoms
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 1695.4773 s ( 99.97%)
TIME: Action Post : 0.5742 s ( 0.03%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0006 s ( 0.00%)
TIME: Other : 0.0014 s ( 0.00%)
TIME: Run Total 1696.0536 s
---------- RUN END ---------------------------------------------------
[reference avg.rst [avg]]
Reading 'avg.rst' as Amber Restart
Setting active reference for distance-based masks: 'avg.rst'
[crdaction crd1 rms ref [avg] :1-2&!@H=]
Using set 'crd1'
----- crd1 (1-100000, 1) -----
RMSD: (:1-2&!@H*), reference is "Cpptraj Generated Restart" (:1-2&!@H*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
Target mask: [:1-2&!@H*](40)
Reference mask: [:1-2&!@H*](40)
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: 15.0420 seconds.
[crdaction crd1 matrix covar :1-2&!@H= name DinucCovar]
Using set 'crd1'
----- crd1 (1-100000, 1) -----
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 40 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 4.5382 seconds.
[runanalysis diagmatrix DinucCovar out evecs.dat vecs 20]
Changed DataFile 'evecs.dat' type to Evecs file for set Modes_00006
DIAGMATRIX: Diagonalizing matrix DinucCovar and writing modes to evecs.dat
Calculating 20 eigenvectors.
Storing modes with name: Modes_00006
Eigenmode calculation for 'DinucCovar'
Calculating eigenvectors and eigenvalues.
Calculating first 20 eigenmodes.
TIME: Total analysis execution time: 0.0074 seconds.
[crdaction crd1 projection T1 modes evecs.dat beg 1 end 10 :1-2&!@H= crdframes 1,50000 out T1.dat]
Using set 'crd1'
----- crd1 (1-50000, 1) -----
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 40 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 1.5935 seconds.
[crdaction crd1 projection T2 modes evecs.dat beg 1 end 10 :1-2&!@H= crdframes 50001,100000 out T2.dat]
Using set 'crd1'
----- crd1 (50001-100000, 1) -----
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 40 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 1.6249 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 -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (2 total):
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.
REFERENCE FRAMES (1 total):
0: [avg]:1
Active reference frame for distance-based masks is 'Cpptraj Generated Restart'
BEGIN TRAJECTORY PROCESSING:
----- traj.1.01 (1-50000, 1) -----
0% 10% 20% 30% 40%
----- traj.1.01 (1-50000, 1) -----
50% 60% 70% 80% 90% 100% Complete.
Read 100000 frames and processed 100000 frames.
TIME: Avg. throughput= 54.6560 frames / second.
ACTION OUTPUT:
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.
Calculating step from min=-8.63153 max=23.4906 bins=400.
Dim Mode1: -8.631529->23.490601, step 0.080305, 400 bins.
Determined bandwidth from normal distribution approximation: 0.833258
Parallelizing calculation with 8 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.
Calculating step from min=-12.9292 max=24.1274 bins=400.
Dim Mode2: -12.929156->24.127396, step 0.092641, 400 bins.
Determined bandwidth from normal distribution approximation: 0.615443
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 11 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.
Calculating step from min=-11.7098 max=12.1331 bins=400.
Dim Mode3: -11.709836->12.133126, step 0.059607, 400 bins.
Determined bandwidth from normal distribution approximation: 0.511006
Parallelizing calculation with 8 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.
Calculating step from min=-11.4055 max=9.17406 bins=400.
Dim Mode4: -11.405457->9.174064, step 0.051449, 400 bins.
Determined bandwidth from normal distribution approximation: 0.374628
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 11 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.
Calculating step from min=-9.47585 max=15.7831 bins=400.
Dim Mode5: -9.475845->15.783084, step 0.063147, 400 bins.
Determined bandwidth from normal distribution approximation: 0.321749
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 41 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.
Calculating step from min=-7.92906 max=7.17295 bins=400.
Dim Mode6: -7.929061->7.172955, step 0.037755, 400 bins.
Determined bandwidth from normal distribution approximation: 0.243934
Parallelizing calculation with 8 threads
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.
Calculating step from min=-9.28242 max=12.0721 bins=400.
Dim Mode7: -9.282417->12.072098, step 0.053386, 400 bins.
Determined bandwidth from normal distribution approximation: 0.217021
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 26 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.
Calculating step from min=-5.95822 max=10.7005 bins=400.
Dim Mode8: -5.958221->10.700508, step 0.041647, 400 bins.
Determined bandwidth from normal distribution approximation: 0.185228
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 21 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.
Calculating step from min=-8.06159 max=6.09368 bins=400.
Dim Mode9: -8.061593->6.093679, step 0.035388, 400 bins.
Determined bandwidth from normal distribution approximation: 0.158522
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 12 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.
Calculating step from min=-5.85699 max=7.72747 bins=400.
Dim Mode10: -5.856986->7.727471, step 0.033961, 400 bins.
Determined bandwidth from normal distribution approximation: 0.136416
Parallelizing calculation with 8 threads
Warning: Kullback-Leibler divergence was undefined for 26 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.
Calculating step from min=-8.63153 max=23.4906 bins=400.
Dim Mode1: -8.631529->23.490601, step 0.080305, 400 bins.
Determined bandwidth from normal distribution approximation: 0.833258
Parallelizing calculation with 8 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.
Calculating step from min=-8.8975 max=23.7833 bins=400.
Dim Mode1: -8.897502->23.783262, step 0.081702, 400 bins.
Determined bandwidth from normal distribution approximation: 0.825851
Parallelizing calculation with 8 threads
12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1]
Calculating step from min=-8.63153 max=23.4906 bins=200.
Dim T1:1: -8.631529->23.490601, step 0.160611, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 30565 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
13: [hist T1:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN1]
Calculating step from min=-13.0194 max=25.1278 bins=200.
Dim T1:2: -13.019365->25.127813, step 0.190736, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 20132 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
14: [hist T1:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN1]
Calculating step from min=-11.7098 max=12.2951 bins=200.
Dim T1:3: -11.709836->12.295072, step 0.120025, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 27276 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
15: [hist T1:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN1]
Calculating step from min=-11.4404 max=9.17406 bins=200.
Dim T1:4: -11.440367->9.174064, step 0.103072, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 4806 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
16: [hist T1:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN1]
Calculating step from min=-9.47585 max=15.7831 bins=200.
Dim T1:5: -9.475845->15.783084, step 0.126295, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 38307 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
17: [hist T2:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN2]
Calculating step from min=-8.8975 max=23.7833 bins=200.
Dim T2:1: -8.897502->23.783262, step 0.163404, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 21756 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
18: [hist T2:2,*,*,*,200 out pca.hist.agr normint name PC2-RUN2]
Calculating step from min=-12.9292 max=24.1274 bins=200.
Dim T2:2: -12.929156->24.127396, step 0.185283, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 45991 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
19: [hist T2:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN2]
Calculating step from min=-11.7801 max=12.1331 bins=200.
Dim T2:3: -11.780095->12.133126, step 0.119566, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 36782 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
20: [hist T2:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN2]
Calculating step from min=-11.4055 max=9.3995 bins=200.
Dim T2:4: -11.405457->9.399501, step 0.104025, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 14317 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
21: [hist T2:5,*,*,*,200 out pca.hist.agr normint name PC5-RUN2]
Calculating step from min=-9.86162 max=15.9119 bins=200.
Dim T2:5: -9.861619->15.911893, step 0.128868, 200 bins.
Hist: 50000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 43855 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 49999
TIME: Analyses took 14.1296 seconds.
DATASETS (58 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
crd1 "crd1" (coordinates), size is 100000 (3.961 GB) Box Coords, 3299 atoms
RMSD_00004 "RMSD_00004" (double, rms), size is 100000
DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 7260
Modes_00006 "Modes_00006" (eigenmodes(covariance)), size is 20
evecs.dat "evecs.dat" (eigenmodes, matrix(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 (6 total):
evecs.dat (Evecs file): Modes_00006
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 TIMING:
TIME: Init : 0.0023 s ( 0.00%)
TIME: Trajectory Process : 1829.6241 s ( 99.17%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 14.1296 s ( 0.77%)
TIME: Data File Write : 1.2682 s ( 0.07%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1845.0243 s
---------- 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 -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (2 total):
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.
REFERENCE FRAMES (1 total):
0: [avg]:1
Active reference frame for distance-based masks is 'Cpptraj Generated Restart'
BEGIN TRAJECTORY PROCESSING:
----- traj.1.01 (1-50000, 1) -----
0% 10% 20% 30% 40%
----- traj.1.01 (1-50000, 1) -----
50% 60% 70% 80% 90% 100% Complete.
Read 100000 frames and processed 100000 frames.
TIME: Avg. throughput= 57.3217 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [modes eigenval name evecs.dat out modes-fraction.dat]
Modes 'evecs.dat'
20 eigenvalues, sum is 120.703160
TIME: Analyses took 0.0000 seconds.
DATASETS (61 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
crd1 "crd1" (coordinates), size is 100000 (3.961 GB) Box Coords, 3299 atoms
RMSD_00004 "RMSD_00004" (double, rms), size is 100000
DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 7260
Modes_00006 "Modes_00006" (eigenmodes(covariance)), size is 20
evecs.dat "evecs.dat" (eigenmodes, matrix(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
XEVAL_00060[Frac] "XEVAL_00060[Frac]" (double), size is 20
XEVAL_00060[Cumulative] "XEVAL_00060[Cumulative]" (double), size is 20
XEVAL_00060[Eigenval] "XEVAL_00060[Eigenval]" (double), size is 20
DATAFILES (7 total):
evecs.dat (Evecs file): Modes_00006
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
modes-fraction.dat (Standard Data File): XEVAL_00060[Frac] XEVAL_00060[Cumulative] XEVAL_00060[Eigenval]
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 1744.5413 s (100.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0798 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 1744.6212 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 5313.1609 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.