CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:07:55 | Available memory: 52642.8 MB INPUT: Reading Input from file 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 [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Reference mask: [:1,2&!@H*](37) RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@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: 0: 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 227214 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 227214 of 227214) Coordinate processing will occur on 227214 frames. REFERENCE FRAMES (1 total): 0: '../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0006 seconds. 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) 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@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 (1-227214, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 227214 frames and processed 227214 frames. TIME: Trajectory processing: 0.8384 s TIME: Avg. throughput= 271002.6001 frames / second. ACTION OUTPUT: DATASETS: 15 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (59 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 227214 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 227214 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 227214 COM "COM" (double, distance), size is 227214 g1 "g1" (double, torsion(gamma)), size is 227214 d1 "d1" (double, torsion(delta)), size is 227214 e1 "e1" (double, torsion(epsilon)), size is 227214 z1 "z1" (double, torsion(zeta)), size is 227214 c1 "c1" (double, torsion(chi)), size is 227214 a2 "a2" (double, torsion(alpha)), size is 227214 b2 "b2" (double, torsion(beta)), size is 227214 g2 "g2" (double, torsion(gamma)), size is 227214 d2 "d2" (double, torsion(delta)), size is 227214 c2 "c2" (double, torsion(chi)), size is 227214 ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Writing results 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 ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 16 analyses: 0: [avg rms_2_aform out avg-rmsd-all.dat] 1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 227214 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 227214.000000 2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Dim COM: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 227214 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 3002 Coordinates out of bounds (-1) Warning: Frame 4171 Coordinates out of bounds (-1) Warning: Frame 9437 Coordinates out of bounds (-1) Warning: Frame 16225 Coordinates out of bounds (-1) Warning: Frame 31903 Coordinates out of bounds (-1) Warning: Frame 34785 Coordinates out of bounds (-1) Warning: Frame 49859 Coordinates out of bounds (-1) Warning: Frame 70858 Coordinates out of bounds (-1) Warning: Frame 74060 Coordinates out of bounds (-1) Warning: Frame 88732 Coordinates out of bounds (-1) Warning: Frame 91914 Coordinates out of bounds (-1) Warning: Frame 93535 Coordinates out of bounds (-1) Warning: Frame 96356 Coordinates out of bounds (-1) Warning: Frame 96735 Coordinates out of bounds (-1) Warning: Frame 98514 Coordinates out of bounds (-1) Warning: Frame 103230 Coordinates out of bounds (-1) Warning: Frame 103735 Coordinates out of bounds (-1) Warning: Frame 107507 Coordinates out of bounds (-1) Warning: Frame 107624 Coordinates out of bounds (-1) Warning: Frame 107837 Coordinates out of bounds (-1) Warning: Frame 110916 Coordinates out of bounds (-1) Warning: Frame 111640 Coordinates out of bounds (-1) Warning: Frame 113703 Coordinates out of bounds (-1) Warning: Frame 114406 Coordinates out of bounds (-1) Warning: Frame 115449 Coordinates out of bounds (-1) Warning: Frame 116715 Coordinates out of bounds (-1) Warning: Frame 117217 Coordinates out of bounds (-1) Warning: Frame 118088 Coordinates out of bounds (-1) Warning: Frame 118339 Coordinates out of bounds (-1) Warning: Frame 118874 Coordinates out of bounds (-1) Warning: Frame 119078 Coordinates out of bounds (-1) Warning: Frame 120638 Coordinates out of bounds (-1) Warning: Frame 120640 Coordinates out of bounds (-1) Warning: Frame 121419 Coordinates out of bounds (-1) Warning: Frame 121565 Coordinates out of bounds (-1) Warning: Frame 121838 Coordinates out of bounds (-1) Warning: Frame 122413 Coordinates out of bounds (-1) Warning: Frame 122467 Coordinates out of bounds (-1) Warning: Frame 122649 Coordinates out of bounds (-1) Warning: Frame 122672 Coordinates out of bounds (-1) Warning: Frame 123295 Coordinates out of bounds (-1) Warning: Frame 123498 Coordinates out of bounds (-1) Warning: Frame 123816 Coordinates out of bounds (-1) Warning: Frame 124451 Coordinates out of bounds (-1) Warning: Frame 124627 Coordinates out of bounds (-1) Warning: Frame 125446 Coordinates out of bounds (-1) Warning: Frame 126406 Coordinates out of bounds (-1) Warning: Frame 126432 Coordinates out of bounds (-1) Warning: Frame 127702 Coordinates out of bounds (-1) Warning: Frame 128238 Coordinates out of bounds (-1) Warning: Frame 128585 Coordinates out of bounds (-1) Warning: Frame 128696 Coordinates out of bounds (-1) Warning: Frame 130461 Coordinates out of bounds (-1) Warning: Frame 130548 Coordinates out of bounds (-1) Warning: Frame 130648 Coordinates out of bounds (-1) Warning: Frame 130740 Coordinates out of bounds (-1) Warning: Frame 132029 Coordinates out of bounds (-1) Warning: Frame 132521 Coordinates out of bounds (-1) Warning: Frame 132662 Coordinates out of bounds (-1) Warning: Frame 133013 Coordinates out of bounds (-1) Warning: Frame 133062 Coordinates out of bounds (-1) Warning: Frame 133135 Coordinates out of bounds (-1) Warning: Frame 133158 Coordinates out of bounds (-1) Warning: Frame 133457 Coordinates out of bounds (-1) Warning: Frame 133631 Coordinates out of bounds (-1) Warning: Frame 134059 Coordinates out of bounds (-1) Warning: Frame 134358 Coordinates out of bounds (-1) Warning: Frame 134551 Coordinates out of bounds (-1) Warning: Frame 135381 Coordinates out of bounds (-1) Warning: Frame 135496 Coordinates out of bounds (-1) Warning: Frame 138196 Coordinates out of bounds (-1) Warning: Frame 138375 Coordinates out of bounds (-1) Warning: Frame 146132 Coordinates out of bounds (-1) Warning: Frame 161754 Coordinates out of bounds (-1) Warning: Frame 162603 Coordinates out of bounds (-1) Warning: Frame 162605 Coordinates out of bounds (-1) Warning: Frame 165187 Coordinates out of bounds (-1) Warning: Frame 165935 Coordinates out of bounds (-1) Warning: Frame 174612 Coordinates out of bounds (-1) Warning: Frame 176518 Coordinates out of bounds (-1) Warning: Frame 176691 Coordinates out of bounds (-1) Warning: Frame 178203 Coordinates out of bounds (-1) Warning: Frame 178204 Coordinates out of bounds (-1) Warning: Frame 178610 Coordinates out of bounds (-1) Warning: Frame 180092 Coordinates out of bounds (-1) Warning: Frame 182049 Coordinates out of bounds (-1) Warning: Frame 191256 Coordinates out of bounds (-1) Warning: Frame 192664 Coordinates out of bounds (-1) Warning: Frame 204875 Coordinates out of bounds (-1) Warning: Frame 204877 Coordinates out of bounds (-1) Warning: Frame 209523 Coordinates out of bounds (-1) Warning: Frame 209830 Coordinates out of bounds (-1) Warning: Frame 209895 Coordinates out of bounds (-1) Warning: Frame 210738 Coordinates out of bounds (-1) Warning: Frame 222063 Coordinates out of bounds (-1) Warning: Frame 222631 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 227118.000000 3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 227214 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 227214.000000 4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 227214 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 227214.000000 5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 227214 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 227214.000000 6: [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm] Dim g1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Dim d1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Dim e1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Dim b2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Dim g2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Dim d2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Dim c2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 227214 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 227214.000000 TIME: Analyses took 0.0372 seconds. DATASETS: 30 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (59 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 227214 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 227214 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 227214 COM "COM" (double, distance), size is 227214 g1 "g1" (double, torsion(gamma)), size is 227214 d1 "d1" (double, torsion(delta)), size is 227214 e1 "e1" (double, torsion(epsilon)), size is 227214 z1 "z1" (double, torsion(zeta)), size is 227214 c1 "c1" (double, torsion(chi)), size is 227214 a2 "a2" (double, torsion(alpha)), size is 227214 b2 "b2" (double, torsion(beta)), size is 227214 g2 "g2" (double, torsion(gamma)), size is 227214 d2 "d2" (double, torsion(delta)), size is 227214 c2 "c2" (double, torsion(chi)), size is 227214 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 Hist_00017 "Hist_00017" (double), size is 100 Hist_00018 "Hist_00018" (double), size is 100 Hist_00019 "Hist_00019" (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: rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM distO2O4-hist.dat (Standard Data File): Hist_00017 distN3-O5p-hist.dat (Standard Data File): Hist_00018 2dhist_rms-dist.gnu (Gnuplot File): Hist_00019 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 avg-rmsd-all.dat (DataSet Average) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1.1910 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.