CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 09:10:49 | Available memory: 15.296 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, 3295 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*](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] Mask [*] corresponds to 3295 atoms. Averaging over 3295 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): 3.956 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= 55.2675 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 (3.956 GB) Box Coords, 3295 atoms RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1809.3814 s ( 99.14%) TIME: Action Post : 15.5925 s ( 0.85%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0145 s ( 0.00%) TIME: Other : 0.0004 s ( 0.00%) TIME: Run Total 1824.9889 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*](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. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 16.4183 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 37 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 4.0487 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: 3.0195 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 37 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 1.3778 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 37 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 7.8885 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, 3295 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= 54.0292 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=-9.31431 max=22.2377 bins=400. Dim Mode1: -9.314315->22.237747, step 0.078880, 400 bins. Determined bandwidth from normal distribution approximation: 0.962044 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=-16.0737 max=12.7552 bins=400. Dim Mode2: -16.073681->12.755168, step 0.072072, 400 bins. Determined bandwidth from normal distribution approximation: 0.586376 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 1 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=-10.1956 max=11.8708 bins=400. Dim Mode3: -10.195579->11.870809, step 0.055166, 400 bins. Determined bandwidth from normal distribution approximation: 0.502012 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=-9.96756 max=14.7045 bins=400. Dim Mode4: -9.967561->14.704493, step 0.061680, 400 bins. Determined bandwidth from normal distribution approximation: 0.341999 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 22 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=-14.6973 max=7.83671 bins=400. Dim Mode5: -14.697274->7.836714, step 0.056335, 400 bins. Determined bandwidth from normal distribution approximation: 0.333212 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. Calculating step from min=-9.15077 max=6.69047 bins=400. Dim Mode6: -9.150768->6.690473, step 0.039603, 400 bins. Determined bandwidth from normal distribution approximation: 0.191236 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 18 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=-6.8982 max=6.4988 bins=400. Dim Mode7: -6.898197->6.498797, step 0.033492, 400 bins. Determined bandwidth from normal distribution approximation: 0.176700 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 12 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=-5.73879 max=5.81998 bins=400. Dim Mode8: -5.738795->5.819977, step 0.028897, 400 bins. Determined bandwidth from normal distribution approximation: 0.159094 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 10 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=-5.49949 max=4.87177 bins=400. Dim Mode9: -5.499485->4.871768, step 0.025928, 400 bins. Determined bandwidth from normal distribution approximation: 0.154587 Parallelizing calculation with 8 threads 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. Calculating step from min=-5.7274 max=6.82925 bins=400. Dim Mode10: -5.727396->6.829251, step 0.031392, 400 bins. Determined bandwidth from normal distribution approximation: 0.149597 Parallelizing calculation with 8 threads Warning: Kullback-Leibler divergence was undefined for 12 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=-9.31431 max=22.2377 bins=400. Dim Mode1: -9.314315->22.237747, step 0.078880, 400 bins. Determined bandwidth from normal distribution approximation: 0.962044 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=-9.36547 max=22.8779 bins=400. Dim Mode1: -9.365469->22.877859, step 0.080608, 400 bins. Determined bandwidth from normal distribution approximation: 0.943135 Parallelizing calculation with 8 threads 12: [hist T1:1,*,*,*,200 out pca.hist.agr normint name PC1-RUN1] Calculating step from min=-9.31431 max=22.2377 bins=200. Dim T1:1: -9.314315->22.237747, step 0.157760, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 17276 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=-16.0738 max=12.9256 bins=200. Dim T1:2: -16.073759->12.925596, step 0.144997, 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 14: [hist T1:3,*,*,*,200 out pca.hist.agr normint name PC3-RUN1] Calculating step from min=-10.3038 max=12.0227 bins=200. Dim T1:3: -10.303836->12.022708, step 0.111633, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 2597 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=-9.96756 max=14.8588 bins=200. Dim T1:4: -9.967561->14.858784, step 0.124132, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 26447 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=-14.6973 max=7.96764 bins=200. Dim T1:5: -14.697274->7.967640, step 0.113325, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 14373 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=-9.36547 max=22.8779 bins=200. Dim T2:1: -9.365469->22.877859, step 0.161217, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 29060 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=-16.0737 max=12.7552 bins=200. Dim T2:2: -16.073681->12.755168, step 0.144144, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 33206 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=-10.1956 max=11.8708 bins=200. Dim T2:3: -10.195579->11.870809, step 0.110332, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 2039 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=-10.077 max=14.7045 bins=200. Dim T2:4: -10.077043->14.704493, step 0.123908, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 2993 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=-14.7285 max=7.83671 bins=200. Dim T2:5: -14.728503->7.836714, step 0.112826, 200 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 200 Warning: Frame 7712 Coordinates out of bounds (200) Histogram: Normalizing integral over bin populations to 1.0 Sum over all bins is 49999 TIME: Analyses took 12.4361 seconds. DATASETS (58 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3.956 GB) Box Coords, 3295 atoms RMSD_00004 "RMSD_00004" (double, rms), size is 100000 DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 6216 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 : 1850.8496 s ( 99.22%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 12.4361 s ( 0.67%) TIME: Data File Write : 2.1487 s ( 0.12%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1865.4368 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, 3295 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= 62.9041 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 133.364490 TIME: Analyses took 0.0000 seconds. DATASETS (61 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 crd1 "crd1" (coordinates), size is 100000 (3.956 GB) Box Coords, 3295 atoms RMSD_00004 "RMSD_00004" (double, rms), size is 100000 DinucCovar "DinucCovar" (double matrix, matrix(covariance)), size is 6216 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 : 1589.7226 s (100.00%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0561 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1589.7789 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 5320.2211 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.