CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/09/16 16:17:38 | Available memory: 15416.8 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,] Reading '../../run1/traj.1.01' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run1/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [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 Netcdf file has overall replica indices. Reading '../../run2/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../run2/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [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', 3301 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 0.0000 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*](41) Reference mask: [:1,2&!@H*](41) 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 3301 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% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 50% 60% 70% 80% 90% 100% Complete. Read 100000 frames and processed 100000 frames. TIME: Trajectory processing: 1167.9949 s TIME: Avg. throughput= 85.6168 frames / second. ACTION OUTPUT: AVERAGE: 100000 frames, [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 (3779.98 MB) Box Coords, 3301 atoms ---------- RUN END --------------------------------------------------- [reference avg.rst [avg]] Reading 'avg.rst' as Amber Restart [crdaction crd1 rms ref [avg] :1-2&!@H=] Using set 'crd1' ----- crd1 (1-100000, 1) ----- Reference mask: [:1-2&!@H*](41) RMSD: (:1-2&!@H*), reference is "avg.rst" (:1-2&!@H*), with fitting. Target mask: [:1-2&!@H*](41) 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: 9.5391 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 41 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 7.9763 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. Storing modes with name: Modes_00005 Eigenmode calculation for 'DinucCovar' Calculating 20 eigenvectors and eigenvalues. TIME: Total analysis execution time: 0.0072 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 41 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 2.8683 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 41 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 2.8693 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 : -16.887835->10.952939, step 0.069602, 400 bins. Determined bandwidth from normal distribution approximation: 0.849314 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. Dim : -27.104099->9.031008, step 0.090338, 400 bins. Determined bandwidth from normal distribution approximation: 0.636838 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 17 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 : -14.381282->9.748597, step 0.060325, 400 bins. Determined bandwidth from normal distribution approximation: 0.458803 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 1 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 : -9.431371->14.583075, step 0.060036, 400 bins. Determined bandwidth from normal distribution approximation: 0.348829 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 17 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 : -10.008802->10.114839, step 0.050309, 400 bins. Determined bandwidth from normal distribution approximation: 0.325897 Parallelizing calculation with 8 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 : -8.894674->7.447001, step 0.040854, 400 bins. Determined bandwidth from normal distribution approximation: 0.227052 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 3 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 : -6.182669->8.257948, step 0.036102, 400 bins. Determined bandwidth from normal distribution approximation: 0.209635 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 4 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 : -6.863472->10.588313, step 0.043629, 400 bins. Determined bandwidth from normal distribution approximation: 0.200918 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 138 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 : -9.365392->5.976506, step 0.038355, 400 bins. Determined bandwidth from normal distribution approximation: 0.181779 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 365 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 : -7.423454->7.136020, step 0.036399, 400 bins. Determined bandwidth from normal distribution approximation: 0.158037 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 42 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 : -16.887835->10.952939, step 0.069602, 400 bins. Determined bandwidth from normal distribution approximation: 0.849314 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. Dim : -17.335917->11.055190, step 0.070978, 400 bins. Determined bandwidth from normal distribution approximation: 0.843587 Parallelizing calculation with 8 threads 12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1] Dim T1:1: -16.887835->10.952939, step 0.139204, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 25724 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: -27.104099->9.031008, step 0.180676, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 33025 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: -15.254955->9.951929, step 0.126034, 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 15: [hist T1:4,*,*,*,200 out pca.hist.agr normint name PC4-RUN1] Dim T1:4: -9.431371->14.583075, step 0.120072, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 45203 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: -10.008802->10.408793, step 0.102088, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 20560 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: -17.335917->11.055190, step 0.141956, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 30270 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: -27.633423->9.264128, step 0.184488, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 8627 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: -14.381282->9.748597, step 0.120649, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 23894 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: -9.444153->14.942718, step 0.121934, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 36374 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: -10.648398->10.114839, step 0.103816, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 35813 Coordinates out of bounds (200) Histogram: Normalizing integral over bin populations to 1.0 Sum over all bins is 49999.000000 TIME: Analyses took 13.8342 seconds. DATASETS: 59 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3779.98 MB) Box Coords, 3301 atoms [avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst' 3301 atoms RMSD_00003 "RMSD_00003" (double, rms), size is 100000 DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 7626 Modes_00005 "Modes_00005" (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: 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 127.194260 TIME: Analyses took 0.0001 seconds. DATASETS: 59 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3779.98 MB) Box Coords, 3301 atoms [avg]:1 "Cpptraj Generated Restart" (reference), size is 1 'avg.rst' 3301 atoms RMSD_00003 "RMSD_00003" (double, rms), size is 100000 DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 7626 Modes_00005 "Modes_00005" (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: 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 modes-fraction.dat (Modes analysis) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1208.6145 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.