CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:06:51 | Available memory: 1.235 GB INPUT: Reading input from 'pt-analysis1.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c0] Reading '../ctraj.c0' as Amber NetCDF [reference ../../../A-form.pdb [a-form]] Reading '../../../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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, 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@N1 :1@C2 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] 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@N1 :2@C2 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 58952 of 58952) Coordinate processing will occur on 58952 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*](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. 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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](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@N1 :2@C2 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c0 (1-58952, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 58952 frames and processed 58952 frames. TIME: Avg. throughput= 119781.9413 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 58952 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 58952 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 58952 COM "COM" (double, distance), size is 58952 g1 "g1" (double, torsion(gamma)), size is 58952 d1 "d1" (double, torsion(delta)), size is 58952 e1 "e1" (double, torsion(epsilon)), size is 58952 z1 "z1" (double, torsion(zeta)), size is 58952 c1 "c1" (double, torsion(chin)), size is 58952 a2 "a2" (double, torsion(alpha)), size is 58952 b2 "b2" (double, torsion(beta)), size is 58952 g2 "g2" (double, torsion(gamma)), size is 58952 d2 "d2" (double, torsion(delta)), size is 58952 c2 "c2" (double, torsion(chin)), size is 58952 RUN TIMING: TIME: Init : 0.0001 s ( 0.02%) TIME: Trajectory Process : 0.4922 s ( 99.97%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4923 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_g1-hist.dat name gamma_1 norm] Hist: dihed_g1-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, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 58952 of 58952) Coordinate processing will occur on 58952 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c0 (1-58952, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 58952 frames and processed 58952 frames. TIME: Avg. throughput= 605735.5404 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: 58952 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 58952 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: 58952 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 12 Coordinates out of bounds (-1) Warning: Frame 503 Coordinates out of bounds (-1) Warning: Frame 2113 Coordinates out of bounds (-1) Warning: Frame 2165 Coordinates out of bounds (-1) Warning: Frame 2406 Coordinates out of bounds (-1) Warning: Frame 3555 Coordinates out of bounds (-1) Warning: Frame 4008 Coordinates out of bounds (-1) Warning: Frame 4351 Coordinates out of bounds (-1) Warning: Frame 4472 Coordinates out of bounds (-1) Warning: Frame 5893 Coordinates out of bounds (-1) Warning: Frame 5894 Coordinates out of bounds (-1) Warning: Frame 7214 Coordinates out of bounds (-1) Warning: Frame 10014 Coordinates out of bounds (-1) Warning: Frame 10015 Coordinates out of bounds (-1) Warning: Frame 12806 Coordinates out of bounds (-1) Warning: Frame 13709 Coordinates out of bounds (-1) Warning: Frame 13734 Coordinates out of bounds (-1) Warning: Frame 15019 Coordinates out of bounds (-1) Warning: Frame 15191 Coordinates out of bounds (-1) Warning: Frame 15820 Coordinates out of bounds (-1) Warning: Frame 15893 Coordinates out of bounds (-1) Warning: Frame 17209 Coordinates out of bounds (-1) Warning: Frame 17416 Coordinates out of bounds (-1) Warning: Frame 17780 Coordinates out of bounds (-1) Warning: Frame 18296 Coordinates out of bounds (-1) Warning: Frame 19361 Coordinates out of bounds (-1) Warning: Frame 19362 Coordinates out of bounds (-1) Warning: Frame 19364 Coordinates out of bounds (-1) Warning: Frame 20103 Coordinates out of bounds (-1) Warning: Frame 20151 Coordinates out of bounds (-1) Warning: Frame 20419 Coordinates out of bounds (-1) Warning: Frame 20426 Coordinates out of bounds (-1) Warning: Frame 20746 Coordinates out of bounds (-1) Warning: Frame 22054 Coordinates out of bounds (-1) Warning: Frame 22191 Coordinates out of bounds (-1) Warning: Frame 23493 Coordinates out of bounds (-1) Warning: Frame 23780 Coordinates out of bounds (-1) Warning: Frame 23959 Coordinates out of bounds (-1) Warning: Frame 25317 Coordinates out of bounds (-1) Warning: Frame 25879 Coordinates out of bounds (-1) Warning: Frame 26730 Coordinates out of bounds (-1) Warning: Frame 28745 Coordinates out of bounds (-1) Warning: Frame 29661 Coordinates out of bounds (-1) Warning: Frame 30967 Coordinates out of bounds (-1) Warning: Frame 31035 Coordinates out of bounds (-1) Warning: Frame 32206 Coordinates out of bounds (-1) Warning: Frame 32369 Coordinates out of bounds (-1) Warning: Frame 33472 Coordinates out of bounds (-1) Warning: Frame 34112 Coordinates out of bounds (-1) Warning: Frame 34885 Coordinates out of bounds (-1) Warning: Frame 35540 Coordinates out of bounds (-1) Warning: Frame 35541 Coordinates out of bounds (-1) Warning: Frame 35569 Coordinates out of bounds (-1) Warning: Frame 38120 Coordinates out of bounds (-1) Warning: Frame 38688 Coordinates out of bounds (-1) Warning: Frame 38880 Coordinates out of bounds (-1) Warning: Frame 38889 Coordinates out of bounds (-1) Warning: Frame 40797 Coordinates out of bounds (-1) Warning: Frame 40928 Coordinates out of bounds (-1) Warning: Frame 40976 Coordinates out of bounds (-1) Warning: Frame 43907 Coordinates out of bounds (-1) Warning: Frame 44132 Coordinates out of bounds (-1) Warning: Frame 45010 Coordinates out of bounds (-1) Warning: Frame 45038 Coordinates out of bounds (-1) Warning: Frame 45141 Coordinates out of bounds (-1) Warning: Frame 46546 Coordinates out of bounds (-1) Warning: Frame 47377 Coordinates out of bounds (-1) Warning: Frame 47379 Coordinates out of bounds (-1) Warning: Frame 47380 Coordinates out of bounds (-1) Warning: Frame 47382 Coordinates out of bounds (-1) Warning: Frame 47994 Coordinates out of bounds (-1) Warning: Frame 50071 Coordinates out of bounds (-1) Warning: Frame 51806 Coordinates out of bounds (-1) Warning: Frame 52124 Coordinates out of bounds (-1) Warning: Frame 54071 Coordinates out of bounds (-1) Warning: Frame 56217 Coordinates out of bounds (-1) Warning: Frame 57553 Coordinates out of bounds (-1) Warning: Frame 57555 Coordinates out of bounds (-1) Warning: Frame 58382 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 58873 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 6: [hist g1,-180,180,1 out dihed_g1-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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 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: 58952 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 58952 TIME: Analyses took 0.0170 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 58952 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 58952 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 58952 COM "COM" (double, distance), size is 58952 g1 "g1" (double, torsion(gamma)), size is 58952 d1 "d1" (double, torsion(delta)), size is 58952 e1 "e1" (double, torsion(epsilon)), size is 58952 z1 "z1" (double, torsion(zeta)), size is 58952 c1 "c1" (double, torsion(chin)), size is 58952 a2 "a2" (double, torsion(alpha)), size is 58952 b2 "b2" (double, torsion(beta)), size is 58952 g2 "g2" (double, torsion(gamma)), size is 58952 d2 "d2" (double, torsion(delta)), size is 58952 c2 "c2" (double, torsion(chin)), size is 58952 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 (16 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_g1-hist.dat (Standard Data File): gamma_1 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_a2-hist.dat (Standard Data File): alpha_2 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 ( 0.07%) TIME: Trajectory Process : 0.0973 s ( 68.45%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0170 s ( 11.97%) TIME: Data File Write : 0.0277 s ( 19.48%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1422 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.6485 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.