CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:16:01 | Available memory: 52200.5 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.c1] Reading '../ctraj.c1' 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*](41) 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,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: 0: 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 115245 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 115245 of 115245) Coordinate processing will occur on 115245 frames. REFERENCE FRAMES (1 total): 0: '../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0005 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*](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 (1-115245, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 115245 frames and processed 115245 frames. TIME: Trajectory processing: 0.4303 s TIME: Avg. throughput= 267827.2631 frames / second. ACTION OUTPUT: DATASETS: 15 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 115245 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 115245 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 115245 COM "COM" (double, distance), size is 115245 g1 "g1" (double, torsion(gamma)), size is 115245 d1 "d1" (double, torsion(delta)), size is 115245 e1 "e1" (double, torsion(epsilon)), size is 115245 z1 "z1" (double, torsion(zeta)), size is 115245 c1 "c1" (double, torsion(chi)), size is 115245 a2 "a2" (double, torsion(alpha)), size is 115245 b2 "b2" (double, torsion(beta)), size is 115245 g2 "g2" (double, torsion(gamma)), size is 115245 d2 "d2" (double, torsion(delta)), size is 115245 c2 "c2" (double, torsion(chi)), size is 115245 ---------- 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: 115245 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 115245.000000 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: 115245 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 4568 Coordinates out of bounds (-1) Warning: Frame 4695 Coordinates out of bounds (-1) Warning: Frame 5141 Coordinates out of bounds (-1) Warning: Frame 12129 Coordinates out of bounds (-1) Warning: Frame 17962 Coordinates out of bounds (-1) Warning: Frame 33883 Coordinates out of bounds (-1) Warning: Frame 43540 Coordinates out of bounds (-1) Warning: Frame 43967 Coordinates out of bounds (-1) Warning: Frame 44810 Coordinates out of bounds (-1) Warning: Frame 44950 Coordinates out of bounds (-1) Warning: Frame 45378 Coordinates out of bounds (-1) Warning: Frame 45801 Coordinates out of bounds (-1) Warning: Frame 47028 Coordinates out of bounds (-1) Warning: Frame 49460 Coordinates out of bounds (-1) Warning: Frame 50706 Coordinates out of bounds (-1) Warning: Frame 51646 Coordinates out of bounds (-1) Warning: Frame 51708 Coordinates out of bounds (-1) Warning: Frame 51895 Coordinates out of bounds (-1) Warning: Frame 52429 Coordinates out of bounds (-1) Warning: Frame 52554 Coordinates out of bounds (-1) Warning: Frame 52658 Coordinates out of bounds (-1) Warning: Frame 52894 Coordinates out of bounds (-1) Warning: Frame 53695 Coordinates out of bounds (-1) Warning: Frame 55046 Coordinates out of bounds (-1) Warning: Frame 55101 Coordinates out of bounds (-1) Warning: Frame 55344 Coordinates out of bounds (-1) Warning: Frame 56051 Coordinates out of bounds (-1) Warning: Frame 56487 Coordinates out of bounds (-1) Warning: Frame 56766 Coordinates out of bounds (-1) Warning: Frame 57781 Coordinates out of bounds (-1) Warning: Frame 57979 Coordinates out of bounds (-1) Warning: Frame 58135 Coordinates out of bounds (-1) Warning: Frame 58751 Coordinates out of bounds (-1) Warning: Frame 58803 Coordinates out of bounds (-1) Warning: Frame 59172 Coordinates out of bounds (-1) Warning: Frame 59274 Coordinates out of bounds (-1) Warning: Frame 60340 Coordinates out of bounds (-1) Warning: Frame 61293 Coordinates out of bounds (-1) Warning: Frame 61408 Coordinates out of bounds (-1) Warning: Frame 61875 Coordinates out of bounds (-1) Warning: Frame 62899 Coordinates out of bounds (-1) Warning: Frame 63033 Coordinates out of bounds (-1) Warning: Frame 63081 Coordinates out of bounds (-1) Warning: Frame 63082 Coordinates out of bounds (-1) Warning: Frame 63295 Coordinates out of bounds (-1) Warning: Frame 63345 Coordinates out of bounds (-1) Warning: Frame 63593 Coordinates out of bounds (-1) Warning: Frame 63622 Coordinates out of bounds (-1) Warning: Frame 63668 Coordinates out of bounds (-1) Warning: Frame 63792 Coordinates out of bounds (-1) Warning: Frame 63805 Coordinates out of bounds (-1) Warning: Frame 63903 Coordinates out of bounds (-1) Warning: Frame 64038 Coordinates out of bounds (-1) Warning: Frame 64256 Coordinates out of bounds (-1) Warning: Frame 64360 Coordinates out of bounds (-1) Warning: Frame 64435 Coordinates out of bounds (-1) Warning: Frame 64599 Coordinates out of bounds (-1) Warning: Frame 64933 Coordinates out of bounds (-1) Warning: Frame 65468 Coordinates out of bounds (-1) Warning: Frame 66337 Coordinates out of bounds (-1) Warning: Frame 66363 Coordinates out of bounds (-1) Warning: Frame 66909 Coordinates out of bounds (-1) Warning: Frame 67114 Coordinates out of bounds (-1) Warning: Frame 67254 Coordinates out of bounds (-1) Warning: Frame 67283 Coordinates out of bounds (-1) Warning: Frame 67655 Coordinates out of bounds (-1) Warning: Frame 68013 Coordinates out of bounds (-1) Warning: Frame 74722 Coordinates out of bounds (-1) Warning: Frame 78699 Coordinates out of bounds (-1) Warning: Frame 106916 Coordinates out of bounds (-1) Warning: Frame 112759 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 115174.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 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: 115245 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 115245.000000 TIME: Analyses took 0.0141 seconds. DATASETS: 30 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 115245 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 115245 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 115245 COM "COM" (double, distance), size is 115245 g1 "g1" (double, torsion(gamma)), size is 115245 d1 "d1" (double, torsion(delta)), size is 115245 e1 "e1" (double, torsion(epsilon)), size is 115245 z1 "z1" (double, torsion(zeta)), size is 115245 c1 "c1" (double, torsion(chi)), size is 115245 a2 "a2" (double, torsion(alpha)), size is 115245 b2 "b2" (double, torsion(beta)), size is 115245 g2 "g2" (double, torsion(gamma)), size is 115245 d2 "d2" (double, torsion(delta)), size is 115245 c2 "c2" (double, torsion(chi)), size is 115245 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: 0.5321 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.