CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:13 | Available memory: 1.735 GB INPUT: Reading input from 'pt-analysis1.in' [parm ../noWAt.topo.hmr] Reading '../noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c1] Reading '../ctraj.c1' as Amber NetCDF [reference ../../../../aa/A-form.pdb [a-form]] Reading '../../../../aa/A-form.pdb' as PDB Setting active reference for distance-based masks: 'A-form.pdb' [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [distance dist_sugar_ox :1@O2' :2@O4'] DISTANCE: :1@O2' to :2@O4', center of mass. [distance dist_N3-O5p :1@N3 :1@O5'] DISTANCE: :1@N3 to :1@O5', center of mass. [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 166306 of 166306) Coordinate processing will occur on 166306 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] 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. 1: [distance dist_sugar_ox :1@O2' :2@O4'] :1@O2' (1 atoms) to :2@O4' (1 atoms), imaged. 2: [distance dist_N3-O5p :1@N3 :1@O5'] :1@N3 (1 atoms) to :1@O5' (1 atoms), imaged. 3: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 8: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- ctraj.c1 (1-166306, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 166306 frames and processed 166306 frames. TIME: Avg. throughput= 171235.1758 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 166306 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 166306 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 166306 COM "COM" (double, distance), size is 166306 g1 "g1" (double, torsion(gamma)), size is 166306 d1 "d1" (double, torsion(delta)), size is 166306 e1 "e1" (double, torsion(epsilon)), size is 166306 z1 "z1" (double, torsion(zeta)), size is 166306 c1 "c1" (double, torsion(chin)), size is 166306 a2 "a2" (double, torsion(alpha)), size is 166306 b2 "b2" (double, torsion(beta)), size is 166306 g2 "g2" (double, torsion(gamma)), size is 166306 d2 "d2" (double, torsion(delta)), size is 166306 c2 "c2" (double, torsion(chin)), size is 166306 RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.9712 s ( 99.98%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.9714 s ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Data set base name 'AVERAGE_00016' Output to to 'avg-rmsd-all.dat' [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets: [ COM ] norm: Sum over bins will be normalized to 1.0. [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_N3-O5p ] norm: Sum over bins will be normalized to 1.0. [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets: [ rms_2_aform dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm] Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets: [ g1 ] norm: Sum over bins will be normalized to 1.0. [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets: [ d1 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets: [ e1 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets: [ z1 ] norm: Sum over bins will be normalized to 1.0. [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets: [ c1 ] norm: Sum over bins will be normalized to 1.0. [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets: [ a2 ] norm: Sum over bins will be normalized to 1.0. [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets: [ b2 ] norm: Sum over bins will be normalized to 1.0. [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets: [ g2 ] norm: Sum over bins will be normalized to 1.0. [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets: [ d2 ] norm: Sum over bins will be normalized to 1.0. [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets: [ c2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 166306 of 166306) Coordinate processing will occur on 166306 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c1 (1-166306, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 166306 frames and processed 166306 frames. TIME: Avg. throughput= 704555.0830 frames / second. ACTION OUTPUT: ANALYSIS: Performing 16 analyses: 0: [avg rms_2_aform out avg-rmsd-all.dat] 1: rms_2_aform 1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Calculating bins from min=0 max=5 step=0.1. Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 50 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Calculating bins from min=0 max=10 step=0.1. Dim COM: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 1890 Coordinates out of bounds (-1) Warning: Frame 4268 Coordinates out of bounds (-1) Warning: Frame 6100 Coordinates out of bounds (-1) Warning: Frame 8646 Coordinates out of bounds (-1) Warning: Frame 29088 Coordinates out of bounds (-1) Warning: Frame 29805 Coordinates out of bounds (-1) Warning: Frame 33443 Coordinates out of bounds (-1) Warning: Frame 43171 Coordinates out of bounds (-1) Warning: Frame 43361 Coordinates out of bounds (-1) Warning: Frame 49280 Coordinates out of bounds (-1) Warning: Frame 50112 Coordinates out of bounds (-1) Warning: Frame 57422 Coordinates out of bounds (-1) Warning: Frame 61483 Coordinates out of bounds (-1) Warning: Frame 63510 Coordinates out of bounds (-1) Warning: Frame 64895 Coordinates out of bounds (-1) Warning: Frame 67450 Coordinates out of bounds (-1) Warning: Frame 68341 Coordinates out of bounds (-1) Warning: Frame 68959 Coordinates out of bounds (-1) Warning: Frame 69724 Coordinates out of bounds (-1) Warning: Frame 71915 Coordinates out of bounds (-1) Warning: Frame 74379 Coordinates out of bounds (-1) Warning: Frame 74460 Coordinates out of bounds (-1) Warning: Frame 77610 Coordinates out of bounds (-1) Warning: Frame 78142 Coordinates out of bounds (-1) Warning: Frame 79001 Coordinates out of bounds (-1) Warning: Frame 81299 Coordinates out of bounds (-1) Warning: Frame 81954 Coordinates out of bounds (-1) Warning: Frame 83962 Coordinates out of bounds (-1) Warning: Frame 94336 Coordinates out of bounds (-1) Warning: Frame 114442 Coordinates out of bounds (-1) Warning: Frame 118282 Coordinates out of bounds (-1) Warning: Frame 119981 Coordinates out of bounds (-1) Warning: Frame 122829 Coordinates out of bounds (-1) Warning: Frame 122931 Coordinates out of bounds (-1) Warning: Frame 124627 Coordinates out of bounds (-1) Warning: Frame 125701 Coordinates out of bounds (-1) Warning: Frame 128976 Coordinates out of bounds (-1) Warning: Frame 133629 Coordinates out of bounds (-1) Warning: Frame 141178 Coordinates out of bounds (-1) Warning: Frame 149476 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166266 3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Calculating bins from min=0 max=10 step=0.1. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 100 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Calculating bins from min=0 max=10 step=0.1. Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 100 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Calculating bins from min=0 max=5 step=0.1. Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Calculating bins from min=0 max=10 step=0.1. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 5000 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 6: [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm] Calculating bins from min=-180 max=180 step=1. Dim g1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Calculating bins from min=-180 max=180 step=1. Dim d1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Calculating bins from min=-180 max=180 step=1. Dim e1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Calculating bins from min=-180 max=180 step=1. Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Calculating bins from min=-180 max=180 step=1. Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Calculating bins from min=-180 max=180 step=1. Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Calculating bins from min=-180 max=180 step=1. Dim b2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Calculating bins from min=-180 max=180 step=1. Dim g2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Calculating bins from min=-180 max=180 step=1. Dim d2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Calculating bins from min=-180 max=180 step=1. Dim c2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 166306 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 166306 TIME: Analyses took 0.0360 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 166306 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 166306 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 166306 COM "COM" (double, distance), size is 166306 g1 "g1" (double, torsion(gamma)), size is 166306 d1 "d1" (double, torsion(delta)), size is 166306 e1 "e1" (double, torsion(epsilon)), size is 166306 z1 "z1" (double, torsion(zeta)), size is 166306 c1 "c1" (double, torsion(chin)), size is 166306 a2 "a2" (double, torsion(alpha)), size is 166306 b2 "b2" (double, torsion(beta)), size is 166306 g2 "g2" (double, torsion(gamma)), size is 166306 d2 "d2" (double, torsion(delta)), size is 166306 c2 "c2" (double, torsion(chin)), size is 166306 AVERAGE_00016[avg] "AVERAGE_00016[avg]" (double), size is 1 AVERAGE_00016[sd] "AVERAGE_00016[sd]" (double), size is 1 AVERAGE_00016[ymin] "AVERAGE_00016[ymin]" (double), size is 1 AVERAGE_00016[ymax] "AVERAGE_00016[ymax]" (double), size is 1 AVERAGE_00016[yminidx] "AVERAGE_00016[yminidx]" (integer), size is 1 AVERAGE_00016[ymaxidx] "AVERAGE_00016[ymaxidx]" (integer), size is 1 AVERAGE_00016[names] "AVERAGE_00016[names]" (string), size is 1 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 Hist_00025 "Hist_00025" (double), size is 100 Hist_00026 "Hist_00026" (double), size is 100 Hist_00027 "Hist_00027" (double matrix), size is 5000 gamma_1 "gamma_1" (double), size is 360 delta_1 "delta_1" (double), size is 360 epsilon_1 "epsilon_1" (double), size is 360 zeta_1 "zeta_1" (double), size is 360 chi_1 "chi_1" (double), size is 360 alpha_2 "alpha_2" (double), size is 360 beta_2 "beta_2" (double), size is 360 gamma_2 "gamma_2" (double), size is 360 delta_2 "delta_2" (double), size is 360 chi_2 "chi_2" (double), size is 360 DATAFILES (15 total): avg-rmsd-all.dat (Standard Data File): AVERAGE_00016[avg] AVERAGE_00016[sd] AVERAGE_00016[ymin] AVERAGE_00016[ymax] AVERAGE_00016[yminidx] AVERAGE_00016[ymaxidx] AVERAGE_00016[names] rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM distO2O4-hist.dat (Standard Data File): Hist_00025 distN3-O5p-hist.dat (Standard Data File): Hist_00026 2dhist_rms-dist.gnu (Gnuplot File): Hist_00027 dihed_a2-hist.dat (Standard Data File): gamma_1 alpha_2 dihed_d1-hist.dat (Standard Data File): delta_1 dihed_e1-hist.dat (Standard Data File): epsilon_1 dihed_z1-hist.dat (Standard Data File): zeta_1 dihed_c1-hist.dat (Standard Data File): chi_1 dihed_b2-hist.dat (Standard Data File): beta_2 dihed_g2-hist.dat (Standard Data File): gamma_2 dihed_d2-hist.dat (Standard Data File): delta_2 dihed_c2-hist.dat (Standard Data File): chi_2 RUN TIMING: TIME: Init : 0.0001 s ( 0.04%) TIME: Trajectory Process : 0.2360 s ( 78.15%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0360 s ( 11.92%) TIME: Data File Write : 0.0298 s ( 9.87%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 0.3020 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1.2861 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.