CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 09:06:27 | Available memory: 15.989 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, 3300 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 3300 atoms. Averaging over 3300 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): 3.962 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= 56.9456 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 (3.962 GB) Box Coords, 3300 atoms RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1756.0617 s ( 99.97%) TIME: Action Post : 0.6114 s ( 0.03%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0008 s ( 0.00%) TIME: Other : 0.0005 s ( 0.00%) TIME: Run Total 1756.6744 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: 19.4767 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: 4.1905 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: 0.0727 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: 1.4352 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: 1.1276 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, 3300 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= 53.6484 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=-9.52502 max=23.4004 bins=400. Dim Mode1: -9.525016->23.400360, step 0.082313, 400 bins. Determined bandwidth from normal distribution approximation: 0.772390 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=-10.7225 max=12.9835 bins=400. Dim Mode2: -10.722539->12.983498, step 0.059265, 400 bins. Determined bandwidth from normal distribution approximation: 0.578488 Parallelizing calculation with 8 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. Calculating step from min=-22.4574 max=10.6774 bins=400. Dim Mode3: -22.457443->10.677372, step 0.082837, 400 bins. Determined bandwidth from normal distribution approximation: 0.556522 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 33 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. Calculating step from min=-10.1256 max=15.9804 bins=400. Dim Mode4: -10.125573->15.980406, step 0.065265, 400 bins. Determined bandwidth from normal distribution approximation: 0.468798 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 46 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=-11.5024 max=9.49479 bins=400. Dim Mode5: -11.502362->9.494788, step 0.052493, 400 bins. Determined bandwidth from normal distribution approximation: 0.379214 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 2 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=-8.27413 max=8.80808 bins=400. Dim Mode6: -8.274128->8.808078, step 0.042706, 400 bins. Determined bandwidth from normal distribution approximation: 0.317614 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 4 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=-9.93323 max=7.89862 bins=400. Dim Mode7: -9.933230->7.898619, step 0.044580, 400 bins. Determined bandwidth from normal distribution approximation: 0.224639 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 56 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=-9.38289 max=7.04158 bins=400. Dim Mode8: -9.382894->7.041579, step 0.041061, 400 bins. Determined bandwidth from normal distribution approximation: 0.217711 Parallelizing calculation with 8 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. Calculating step from min=-9.04119 max=6.37332 bins=400. Dim Mode9: -9.041191->6.373319, step 0.038536, 400 bins. Determined bandwidth from normal distribution approximation: 0.181303 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 47 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=-6.09923 max=6.79872 bins=400. Dim Mode10: -6.099234->6.798720, step 0.032245, 400 bins. Determined bandwidth from normal distribution approximation: 0.153089 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 27 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=-9.56944 max=23.4004 bins=400. Dim Mode1: -9.569444->23.400360, step 0.082425, 400 bins. Determined bandwidth from normal distribution approximation: 0.772390 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=-9.52502 max=23.5588 bins=400. Dim Mode1: -9.525016->23.558811, step 0.082710, 400 bins. Determined bandwidth from normal distribution approximation: 0.772704 Parallelizing calculation with 8 threads 12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1] Calculating step from min=-9.56944 max=23.4004 bins=200. Dim T1:1: -9.569444->23.400360, step 0.164849, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 12546 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=-10.7225 max=13.8048 bins=200. Dim T1:2: -10.722539->13.804757, step 0.122636, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 20798 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=-22.4795 max=10.9144 bins=200. Dim T1:3: -22.479513->10.914370, step 0.166969, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 41605 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=-10.1256 max=16.0568 bins=200. Dim T1:4: -10.125573->16.056839, step 0.130912, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 1594 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=-11.53 max=9.49479 bins=200. Dim T1:5: -11.529974->9.494788, step 0.105124, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 23984 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=-9.52502 max=23.5588 bins=200. Dim T2:1: -9.525016->23.558811, step 0.165419, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 3907 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=-10.9864 max=12.9835 bins=200. Dim T2:2: -10.986363->12.983498, step 0.119849, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 8798 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=-22.4574 max=10.6774 bins=200. Dim T2:3: -22.457443->10.677372, step 0.165674, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 28358 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=-10.1753 max=15.9804 bins=200. Dim T2:4: -10.175278->15.980406, step 0.130778, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 19233 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=-11.5024 max=9.53036 bins=200. Dim T2:5: -11.502362->9.530362, step 0.105164, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 16888 Coordinates out of bounds (200) Histogram: Normalizing integral over bin populations to 1.0 Sum over all bins is 49999 TIME: Analyses took 22.9903 seconds. DATASETS (58 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3.962 GB) Box Coords, 3300 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 : 0.0022 s ( 0.00%) TIME: Trajectory Process : 1863.9882 s ( 98.67%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 22.9903 s ( 1.22%) TIME: Data File Write : 2.1593 s ( 0.11%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1889.1400 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, 3300 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= 58.1778 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 133.882230 TIME: Analyses took 0.0000 seconds. DATASETS (61 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3.962 GB) Box Coords, 3300 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 : 1718.8691 s (100.00%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0616 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1718.9309 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 5398.9416 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.