CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:02:41 | Available memory: 54714 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.c2] Reading '../ctraj.c2' 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, 99498 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 99498 of 99498) Coordinate processing will occur on 99498 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.c2 (1-99498, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 99498 frames and processed 99498 frames. TIME: Trajectory processing: 0.3771 s TIME: Avg. throughput= 263831.5475 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 99498 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 99498 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 99498 COM "COM" (double, distance), size is 99498 g1 "g1" (double, torsion(gamma)), size is 99498 d1 "d1" (double, torsion(delta)), size is 99498 e1 "e1" (double, torsion(epsilon)), size is 99498 z1 "z1" (double, torsion(zeta)), size is 99498 c1 "c1" (double, torsion(chi)), size is 99498 a2 "a2" (double, torsion(alpha)), size is 99498 b2 "b2" (double, torsion(beta)), size is 99498 g2 "g2" (double, torsion(gamma)), size is 99498 d2 "d2" (double, torsion(delta)), size is 99498 c2 "c2" (double, torsion(chi)), size is 99498 ---------- 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: 99498 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 99498.000000 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: 99498 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 202 Coordinates out of bounds (-1) Warning: Frame 903 Coordinates out of bounds (-1) Warning: Frame 1005 Coordinates out of bounds (-1) Warning: Frame 1404 Coordinates out of bounds (-1) Warning: Frame 1981 Coordinates out of bounds (-1) Warning: Frame 2911 Coordinates out of bounds (-1) Warning: Frame 3587 Coordinates out of bounds (-1) Warning: Frame 4244 Coordinates out of bounds (-1) Warning: Frame 5667 Coordinates out of bounds (-1) Warning: Frame 9094 Coordinates out of bounds (-1) Warning: Frame 12991 Coordinates out of bounds (-1) Warning: Frame 14598 Coordinates out of bounds (-1) Warning: Frame 14938 Coordinates out of bounds (-1) Warning: Frame 15989 Coordinates out of bounds (-1) Warning: Frame 17055 Coordinates out of bounds (-1) Warning: Frame 18776 Coordinates out of bounds (-1) Warning: Frame 19026 Coordinates out of bounds (-1) Warning: Frame 19535 Coordinates out of bounds (-1) Warning: Frame 21582 Coordinates out of bounds (-1) Warning: Frame 22049 Coordinates out of bounds (-1) Warning: Frame 23716 Coordinates out of bounds (-1) Warning: Frame 25005 Coordinates out of bounds (-1) Warning: Frame 25497 Coordinates out of bounds (-1) Warning: Frame 27203 Coordinates out of bounds (-1) Warning: Frame 28013 Coordinates out of bounds (-1) Warning: Frame 28917 Coordinates out of bounds (-1) Warning: Frame 29720 Coordinates out of bounds (-1) Warning: Frame 30454 Coordinates out of bounds (-1) Warning: Frame 32776 Coordinates out of bounds (-1) Warning: Frame 33355 Coordinates out of bounds (-1) Warning: Frame 33359 Coordinates out of bounds (-1) Warning: Frame 33474 Coordinates out of bounds (-1) Warning: Frame 34631 Coordinates out of bounds (-1) Warning: Frame 34965 Coordinates out of bounds (-1) Warning: Frame 35625 Coordinates out of bounds (-1) Warning: Frame 35824 Coordinates out of bounds (-1) Warning: Frame 36200 Coordinates out of bounds (-1) Warning: Frame 36691 Coordinates out of bounds (-1) Warning: Frame 37001 Coordinates out of bounds (-1) Warning: Frame 37463 Coordinates out of bounds (-1) Warning: Frame 37781 Coordinates out of bounds (-1) Warning: Frame 38046 Coordinates out of bounds (-1) Warning: Frame 38130 Coordinates out of bounds (-1) Warning: Frame 38131 Coordinates out of bounds (-1) Warning: Frame 38135 Coordinates out of bounds (-1) Warning: Frame 38710 Coordinates out of bounds (-1) Warning: Frame 39323 Coordinates out of bounds (-1) Warning: Frame 39338 Coordinates out of bounds (-1) Warning: Frame 40084 Coordinates out of bounds (-1) Warning: Frame 40340 Coordinates out of bounds (-1) Warning: Frame 40342 Coordinates out of bounds (-1) Warning: Frame 42126 Coordinates out of bounds (-1) Warning: Frame 43226 Coordinates out of bounds (-1) Warning: Frame 43840 Coordinates out of bounds (-1) Warning: Frame 45482 Coordinates out of bounds (-1) Warning: Frame 45884 Coordinates out of bounds (-1) Warning: Frame 46302 Coordinates out of bounds (-1) Warning: Frame 47329 Coordinates out of bounds (-1) Warning: Frame 48292 Coordinates out of bounds (-1) Warning: Frame 48612 Coordinates out of bounds (-1) Warning: Frame 48658 Coordinates out of bounds (-1) Warning: Frame 48672 Coordinates out of bounds (-1) Warning: Frame 49657 Coordinates out of bounds (-1) Warning: Frame 51667 Coordinates out of bounds (-1) Warning: Frame 52005 Coordinates out of bounds (-1) Warning: Frame 52444 Coordinates out of bounds (-1) Warning: Frame 52507 Coordinates out of bounds (-1) Warning: Frame 52859 Coordinates out of bounds (-1) Warning: Frame 53675 Coordinates out of bounds (-1) Warning: Frame 54520 Coordinates out of bounds (-1) Warning: Frame 54876 Coordinates out of bounds (-1) Warning: Frame 54914 Coordinates out of bounds (-1) Warning: Frame 56410 Coordinates out of bounds (-1) Warning: Frame 56444 Coordinates out of bounds (-1) Warning: Frame 56550 Coordinates out of bounds (-1) Warning: Frame 56597 Coordinates out of bounds (-1) Warning: Frame 56611 Coordinates out of bounds (-1) Warning: Frame 56726 Coordinates out of bounds (-1) Warning: Frame 56780 Coordinates out of bounds (-1) Warning: Frame 56833 Coordinates out of bounds (-1) Warning: Frame 57285 Coordinates out of bounds (-1) Warning: Frame 57429 Coordinates out of bounds (-1) Warning: Frame 57739 Coordinates out of bounds (-1) Warning: Frame 58815 Coordinates out of bounds (-1) Warning: Frame 58989 Coordinates out of bounds (-1) Warning: Frame 59952 Coordinates out of bounds (-1) Warning: Frame 60000 Coordinates out of bounds (-1) Warning: Frame 60162 Coordinates out of bounds (-1) Warning: Frame 66046 Coordinates out of bounds (-1) Warning: Frame 68419 Coordinates out of bounds (-1) Warning: Frame 68630 Coordinates out of bounds (-1) Warning: Frame 68651 Coordinates out of bounds (-1) Warning: Frame 70670 Coordinates out of bounds (-1) Warning: Frame 71303 Coordinates out of bounds (-1) Warning: Frame 72034 Coordinates out of bounds (-1) Warning: Frame 72145 Coordinates out of bounds (-1) Warning: Frame 74227 Coordinates out of bounds (-1) Warning: Frame 75557 Coordinates out of bounds (-1) Warning: Frame 78402 Coordinates out of bounds (-1) Warning: Frame 83375 Coordinates out of bounds (-1) Warning: Frame 84658 Coordinates out of bounds (-1) Warning: Frame 85139 Coordinates out of bounds (-1) Warning: Frame 85724 Coordinates out of bounds (-1) Warning: Frame 85725 Coordinates out of bounds (-1) Warning: Frame 85768 Coordinates out of bounds (-1) Warning: Frame 86926 Coordinates out of bounds (-1) Warning: Frame 87724 Coordinates out of bounds (-1) Warning: Frame 90146 Coordinates out of bounds (-1) Warning: Frame 90945 Coordinates out of bounds (-1) Warning: Frame 91006 Coordinates out of bounds (-1) Warning: Frame 92217 Coordinates out of bounds (-1) Warning: Frame 93958 Coordinates out of bounds (-1) Warning: Frame 93985 Coordinates out of bounds (-1) Warning: Frame 94712 Coordinates out of bounds (-1) Warning: Frame 99082 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 99383.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 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: 99498 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 99498.000000 TIME: Analyses took 0.0134 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 99498 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 99498 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 99498 COM "COM" (double, distance), size is 99498 g1 "g1" (double, torsion(gamma)), size is 99498 d1 "d1" (double, torsion(delta)), size is 99498 e1 "e1" (double, torsion(epsilon)), size is 99498 z1 "z1" (double, torsion(zeta)), size is 99498 c1 "c1" (double, torsion(chi)), size is 99498 a2 "a2" (double, torsion(alpha)), size is 99498 b2 "b2" (double, torsion(beta)), size is 99498 g2 "g2" (double, torsion(gamma)), size is 99498 d2 "d2" (double, torsion(delta)), size is 99498 c2 "c2" (double, torsion(chi)), size is 99498 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: 0.4930 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.