CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 11:42:06 | Available memory: 1.753 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.c3] Reading '../ctraj.c3' 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 :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] 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,N2,H21,H22,N7,C8,H8,N9,O6, 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 chin] 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 chin] 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, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) Coordinate processing will occur on 71210 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (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 chin] [: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 chin] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- ctraj.c3 (1-71210, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 71210 frames and processed 71210 frames. TIME: Avg. throughput= 137001.3236 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 71210 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 71210 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 71210 COM "COM" (double, distance), size is 71210 g1 "g1" (double, torsion(gamma)), size is 71210 d1 "d1" (double, torsion(delta)), size is 71210 e1 "e1" (double, torsion(epsilon)), size is 71210 z1 "z1" (double, torsion(zeta)), size is 71210 c1 "c1" (double, torsion(chin)), size is 71210 a2 "a2" (double, torsion(alpha)), size is 71210 b2 "b2" (double, torsion(beta)), size is 71210 g2 "g2" (double, torsion(gamma)), size is 71210 d2 "d2" (double, torsion(delta)), size is 71210 c2 "c2" (double, torsion(chin)), size is 71210 RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.5198 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 0.5199 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, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) Coordinate processing will occur on 71210 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c3 (1-71210, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 71210 frames and processed 71210 frames. TIME: Avg. throughput= 965258.2923 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: 71210 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 71210 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: 71210 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 78 Coordinates out of bounds (-1) Warning: Frame 143 Coordinates out of bounds (-1) Warning: Frame 144 Coordinates out of bounds (-1) Warning: Frame 145 Coordinates out of bounds (-1) Warning: Frame 231 Coordinates out of bounds (-1) Warning: Frame 331 Coordinates out of bounds (-1) Warning: Frame 820 Coordinates out of bounds (-1) Warning: Frame 823 Coordinates out of bounds (-1) Warning: Frame 852 Coordinates out of bounds (-1) Warning: Frame 902 Coordinates out of bounds (-1) Warning: Frame 994 Coordinates out of bounds (-1) Warning: Frame 1022 Coordinates out of bounds (-1) Warning: Frame 1023 Coordinates out of bounds (-1) Warning: Frame 1158 Coordinates out of bounds (-1) Warning: Frame 1296 Coordinates out of bounds (-1) Warning: Frame 1431 Coordinates out of bounds (-1) Warning: Frame 1471 Coordinates out of bounds (-1) Warning: Frame 1806 Coordinates out of bounds (-1) Warning: Frame 1832 Coordinates out of bounds (-1) Warning: Frame 1839 Coordinates out of bounds (-1) Warning: Frame 1963 Coordinates out of bounds (-1) Warning: Frame 1967 Coordinates out of bounds (-1) Warning: Frame 1968 Coordinates out of bounds (-1) Warning: Frame 2017 Coordinates out of bounds (-1) Warning: Frame 2212 Coordinates out of bounds (-1) Warning: Frame 2385 Coordinates out of bounds (-1) Warning: Frame 2399 Coordinates out of bounds (-1) Warning: Frame 2403 Coordinates out of bounds (-1) Warning: Frame 2696 Coordinates out of bounds (-1) Warning: Frame 2862 Coordinates out of bounds (-1) Warning: Frame 3202 Coordinates out of bounds (-1) Warning: Frame 3218 Coordinates out of bounds (-1) Warning: Frame 3274 Coordinates out of bounds (-1) Warning: Frame 3298 Coordinates out of bounds (-1) Warning: Frame 3421 Coordinates out of bounds (-1) Warning: Frame 3456 Coordinates out of bounds (-1) Warning: Frame 3671 Coordinates out of bounds (-1) Warning: Frame 3914 Coordinates out of bounds (-1) Warning: Frame 4214 Coordinates out of bounds (-1) Warning: Frame 4238 Coordinates out of bounds (-1) Warning: Frame 4413 Coordinates out of bounds (-1) Warning: Frame 4414 Coordinates out of bounds (-1) Warning: Frame 4529 Coordinates out of bounds (-1) Warning: Frame 4536 Coordinates out of bounds (-1) Warning: Frame 4760 Coordinates out of bounds (-1) Warning: Frame 4761 Coordinates out of bounds (-1) Warning: Frame 4838 Coordinates out of bounds (-1) Warning: Frame 5258 Coordinates out of bounds (-1) Warning: Frame 5358 Coordinates out of bounds (-1) Warning: Frame 5360 Coordinates out of bounds (-1) Warning: Frame 5619 Coordinates out of bounds (-1) Warning: Frame 5688 Coordinates out of bounds (-1) Warning: Frame 5770 Coordinates out of bounds (-1) Warning: Frame 5898 Coordinates out of bounds (-1) Warning: Frame 6744 Coordinates out of bounds (-1) Warning: Frame 6745 Coordinates out of bounds (-1) Warning: Frame 6904 Coordinates out of bounds (-1) Warning: Frame 6984 Coordinates out of bounds (-1) Warning: Frame 6986 Coordinates out of bounds (-1) Warning: Frame 6987 Coordinates out of bounds (-1) Warning: Frame 7224 Coordinates out of bounds (-1) Warning: Frame 7264 Coordinates out of bounds (-1) Warning: Frame 7265 Coordinates out of bounds (-1) Warning: Frame 7523 Coordinates out of bounds (-1) Warning: Frame 7556 Coordinates out of bounds (-1) Warning: Frame 7770 Coordinates out of bounds (-1) Warning: Frame 7873 Coordinates out of bounds (-1) Warning: Frame 8436 Coordinates out of bounds (-1) Warning: Frame 8439 Coordinates out of bounds (-1) Warning: Frame 8447 Coordinates out of bounds (-1) Warning: Frame 8448 Coordinates out of bounds (-1) Warning: Frame 8450 Coordinates out of bounds (-1) Warning: Frame 8553 Coordinates out of bounds (-1) Warning: Frame 8562 Coordinates out of bounds (-1) Warning: Frame 8730 Coordinates out of bounds (-1) Warning: Frame 8758 Coordinates out of bounds (-1) Warning: Frame 8790 Coordinates out of bounds (-1) Warning: Frame 8798 Coordinates out of bounds (-1) Warning: Frame 8800 Coordinates out of bounds (-1) Warning: Frame 9246 Coordinates out of bounds (-1) Warning: Frame 9278 Coordinates out of bounds (-1) Warning: Frame 9280 Coordinates out of bounds (-1) Warning: Frame 9287 Coordinates out of bounds (-1) Warning: Frame 9451 Coordinates out of bounds (-1) Warning: Frame 9571 Coordinates out of bounds (-1) Warning: Frame 9662 Coordinates out of bounds (-1) Warning: Frame 9663 Coordinates out of bounds (-1) Warning: Frame 9664 Coordinates out of bounds (-1) Warning: Frame 9968 Coordinates out of bounds (-1) Warning: Frame 10501 Coordinates out of bounds (-1) Warning: Frame 10719 Coordinates out of bounds (-1) Warning: Frame 10803 Coordinates out of bounds (-1) Warning: Frame 10836 Coordinates out of bounds (-1) Warning: Frame 11010 Coordinates out of bounds (-1) Warning: Frame 11117 Coordinates out of bounds (-1) Warning: Frame 11290 Coordinates out of bounds (-1) Warning: Frame 11697 Coordinates out of bounds (-1) Warning: Frame 11845 Coordinates out of bounds (-1) Warning: Frame 11848 Coordinates out of bounds (-1) Warning: Frame 12015 Coordinates out of bounds (-1) Warning: Frame 12129 Coordinates out of bounds (-1) Warning: Frame 12160 Coordinates out of bounds (-1) Warning: Frame 12178 Coordinates out of bounds (-1) Warning: Frame 12208 Coordinates out of bounds (-1) Warning: Frame 12261 Coordinates out of bounds (-1) Warning: Frame 12262 Coordinates out of bounds (-1) Warning: Frame 12312 Coordinates out of bounds (-1) Warning: Frame 12485 Coordinates out of bounds (-1) Warning: Frame 12555 Coordinates out of bounds (-1) Warning: Frame 12713 Coordinates out of bounds (-1) Warning: Frame 12919 Coordinates out of bounds (-1) Warning: Frame 13086 Coordinates out of bounds (-1) Warning: Frame 13088 Coordinates out of bounds (-1) Warning: Frame 13183 Coordinates out of bounds (-1) Warning: Frame 13260 Coordinates out of bounds (-1) Warning: Frame 13418 Coordinates out of bounds (-1) Warning: Frame 13448 Coordinates out of bounds (-1) Warning: Frame 13450 Coordinates out of bounds (-1) Warning: Frame 13452 Coordinates out of bounds (-1) Warning: Frame 13621 Coordinates out of bounds (-1) Warning: Frame 13871 Coordinates out of bounds (-1) Warning: Frame 14100 Coordinates out of bounds (-1) Warning: Frame 14382 Coordinates out of bounds (-1) Warning: Frame 14384 Coordinates out of bounds (-1) Warning: Frame 14413 Coordinates out of bounds (-1) Warning: Frame 14414 Coordinates out of bounds (-1) Warning: Frame 14435 Coordinates out of bounds (-1) Warning: Frame 14538 Coordinates out of bounds (-1) Warning: Frame 14547 Coordinates out of bounds (-1) Warning: Frame 14959 Coordinates out of bounds (-1) Warning: Frame 14995 Coordinates out of bounds (-1) Warning: Frame 15233 Coordinates out of bounds (-1) Warning: Frame 15269 Coordinates out of bounds (-1) Warning: Frame 15913 Coordinates out of bounds (-1) Warning: Frame 15915 Coordinates out of bounds (-1) Warning: Frame 15916 Coordinates out of bounds (-1) Warning: Frame 16119 Coordinates out of bounds (-1) Warning: Frame 16122 Coordinates out of bounds (-1) Warning: Frame 16159 Coordinates out of bounds (-1) Warning: Frame 16160 Coordinates out of bounds (-1) Warning: Frame 16283 Coordinates out of bounds (-1) Warning: Frame 16284 Coordinates out of bounds (-1) Warning: Frame 16384 Coordinates out of bounds (-1) Warning: Frame 16439 Coordinates out of bounds (-1) Warning: Frame 16853 Coordinates out of bounds (-1) Warning: Frame 17182 Coordinates out of bounds (-1) Warning: Frame 17209 Coordinates out of bounds (-1) Warning: Frame 17329 Coordinates out of bounds (-1) Warning: Frame 17444 Coordinates out of bounds (-1) Warning: Frame 17453 Coordinates out of bounds (-1) Warning: Frame 17695 Coordinates out of bounds (-1) Warning: Frame 17696 Coordinates out of bounds (-1) Warning: Frame 17697 Coordinates out of bounds (-1) Warning: Frame 17825 Coordinates out of bounds (-1) Warning: Frame 17987 Coordinates out of bounds (-1) Warning: Frame 18459 Coordinates out of bounds (-1) Warning: Frame 18481 Coordinates out of bounds (-1) Warning: Frame 18765 Coordinates out of bounds (-1) Warning: Frame 18915 Coordinates out of bounds (-1) Warning: Frame 18946 Coordinates out of bounds (-1) Warning: Frame 19346 Coordinates out of bounds (-1) Warning: Frame 19347 Coordinates out of bounds (-1) Warning: Frame 19457 Coordinates out of bounds (-1) Warning: Frame 19458 Coordinates out of bounds (-1) Warning: Frame 19461 Coordinates out of bounds (-1) Warning: Frame 19485 Coordinates out of bounds (-1) Warning: Frame 19622 Coordinates out of bounds (-1) Warning: Frame 19663 Coordinates out of bounds (-1) Warning: Frame 19802 Coordinates out of bounds (-1) Warning: Frame 19811 Coordinates out of bounds (-1) Warning: Frame 19814 Coordinates out of bounds (-1) Warning: Frame 20236 Coordinates out of bounds (-1) Warning: Frame 20364 Coordinates out of bounds (-1) Warning: Frame 20504 Coordinates out of bounds (-1) Warning: Frame 20726 Coordinates out of bounds (-1) Warning: Frame 20730 Coordinates out of bounds (-1) Warning: Frame 20790 Coordinates out of bounds (-1) Warning: Frame 20810 Coordinates out of bounds (-1) Warning: Frame 20813 Coordinates out of bounds (-1) Warning: Frame 21033 Coordinates out of bounds (-1) Warning: Frame 21092 Coordinates out of bounds (-1) Warning: Frame 21093 Coordinates out of bounds (-1) Warning: Frame 21586 Coordinates out of bounds (-1) Warning: Frame 21587 Coordinates out of bounds (-1) Warning: Frame 21610 Coordinates out of bounds (-1) Warning: Frame 21623 Coordinates out of bounds (-1) Warning: Frame 21952 Coordinates out of bounds (-1) Warning: Frame 22141 Coordinates out of bounds (-1) Warning: Frame 22392 Coordinates out of bounds (-1) Warning: Frame 22514 Coordinates out of bounds (-1) Warning: Frame 22863 Coordinates out of bounds (-1) Warning: Frame 22866 Coordinates out of bounds (-1) Warning: Frame 22875 Coordinates out of bounds (-1) Warning: Frame 22970 Coordinates out of bounds (-1) Warning: Frame 23218 Coordinates out of bounds (-1) Warning: Frame 23219 Coordinates out of bounds (-1) Warning: Frame 23228 Coordinates out of bounds (-1) Warning: Frame 23229 Coordinates out of bounds (-1) Warning: Frame 23351 Coordinates out of bounds (-1) Warning: Frame 23417 Coordinates out of bounds (-1) Warning: Frame 23419 Coordinates out of bounds (-1) Warning: Frame 23854 Coordinates out of bounds (-1) Warning: Frame 23981 Coordinates out of bounds (-1) Warning: Frame 24010 Coordinates out of bounds (-1) Warning: Frame 24416 Coordinates out of bounds (-1) Warning: Frame 24417 Coordinates out of bounds (-1) Warning: Frame 24513 Coordinates out of bounds (-1) Warning: Frame 24737 Coordinates out of bounds (-1) Warning: Frame 24968 Coordinates out of bounds (-1) Warning: Frame 25066 Coordinates out of bounds (-1) Warning: Frame 25094 Coordinates out of bounds (-1) Warning: Frame 25197 Coordinates out of bounds (-1) Warning: Frame 25271 Coordinates out of bounds (-1) Warning: Frame 25272 Coordinates out of bounds (-1) Warning: Frame 25277 Coordinates out of bounds (-1) Warning: Frame 25558 Coordinates out of bounds (-1) Warning: Frame 25578 Coordinates out of bounds (-1) Warning: Frame 25953 Coordinates out of bounds (-1) Warning: Frame 26284 Coordinates out of bounds (-1) Warning: Frame 26625 Coordinates out of bounds (-1) Warning: Frame 26809 Coordinates out of bounds (-1) Warning: Frame 27180 Coordinates out of bounds (-1) Warning: Frame 27358 Coordinates out of bounds (-1) Warning: Frame 27364 Coordinates out of bounds (-1) Warning: Frame 27452 Coordinates out of bounds (-1) Warning: Frame 27618 Coordinates out of bounds (-1) Warning: Frame 27780 Coordinates out of bounds (-1) Warning: Frame 27841 Coordinates out of bounds (-1) Warning: Frame 27859 Coordinates out of bounds (-1) Warning: Frame 27993 Coordinates out of bounds (-1) Warning: Frame 28036 Coordinates out of bounds (-1) Warning: Frame 28059 Coordinates out of bounds (-1) Warning: Frame 28093 Coordinates out of bounds (-1) Warning: Frame 28097 Coordinates out of bounds (-1) Warning: Frame 28134 Coordinates out of bounds (-1) Warning: Frame 28148 Coordinates out of bounds (-1) Warning: Frame 28157 Coordinates out of bounds (-1) Warning: Frame 28180 Coordinates out of bounds (-1) Warning: Frame 28194 Coordinates out of bounds (-1) Warning: Frame 28256 Coordinates out of bounds (-1) Warning: Frame 28257 Coordinates out of bounds (-1) Warning: Frame 28258 Coordinates out of bounds (-1) Warning: Frame 28286 Coordinates out of bounds (-1) Warning: Frame 28287 Coordinates out of bounds (-1) Warning: Frame 28298 Coordinates out of bounds (-1) Warning: Frame 28299 Coordinates out of bounds (-1) Warning: Frame 28316 Coordinates out of bounds (-1) Warning: Frame 28317 Coordinates out of bounds (-1) Warning: Frame 28331 Coordinates out of bounds (-1) Warning: Frame 28336 Coordinates out of bounds (-1) Warning: Frame 28371 Coordinates out of bounds (-1) Warning: Frame 28374 Coordinates out of bounds (-1) Warning: Frame 28397 Coordinates out of bounds (-1) Warning: Frame 28402 Coordinates out of bounds (-1) Warning: Frame 28404 Coordinates out of bounds (-1) Warning: Frame 28416 Coordinates out of bounds (-1) Warning: Frame 28425 Coordinates out of bounds (-1) Warning: Frame 28458 Coordinates out of bounds (-1) Warning: Frame 28463 Coordinates out of bounds (-1) Warning: Frame 28464 Coordinates out of bounds (-1) Warning: Frame 28469 Coordinates out of bounds (-1) Warning: Frame 28479 Coordinates out of bounds (-1) Warning: Frame 28482 Coordinates out of bounds (-1) Warning: Frame 28492 Coordinates out of bounds (-1) Warning: Frame 28493 Coordinates out of bounds (-1) Warning: Frame 28498 Coordinates out of bounds (-1) Warning: Frame 28538 Coordinates out of bounds (-1) Warning: Frame 28573 Coordinates out of bounds (-1) Warning: Frame 28580 Coordinates out of bounds (-1) Warning: Frame 28604 Coordinates out of bounds (-1) Warning: Frame 28612 Coordinates out of bounds (-1) Warning: Frame 28627 Coordinates out of bounds (-1) Warning: Frame 28628 Coordinates out of bounds (-1) Warning: Frame 28629 Coordinates out of bounds (-1) Warning: Frame 28689 Coordinates out of bounds (-1) Warning: Frame 28704 Coordinates out of bounds (-1) Warning: Frame 28724 Coordinates out of bounds (-1) Warning: Frame 28729 Coordinates out of bounds (-1) Warning: Frame 28730 Coordinates out of bounds (-1) Warning: Frame 28762 Coordinates out of bounds (-1) Warning: Frame 28767 Coordinates out of bounds (-1) Warning: Frame 28768 Coordinates out of bounds (-1) Warning: Frame 28785 Coordinates out of bounds (-1) Warning: Frame 28796 Coordinates out of bounds (-1) Warning: Frame 28801 Coordinates out of bounds (-1) Warning: Frame 28851 Coordinates out of bounds (-1) Warning: Frame 28853 Coordinates out of bounds (-1) Warning: Frame 28856 Coordinates out of bounds (-1) Warning: Frame 28869 Coordinates out of bounds (-1) 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out of bounds (-1) Warning: Frame 29782 Coordinates out of bounds (-1) Warning: Frame 29804 Coordinates out of bounds (-1) Warning: Frame 29807 Coordinates out of bounds (-1) Warning: Frame 29822 Coordinates out of bounds (-1) Warning: Frame 29824 Coordinates out of bounds (-1) Warning: Frame 29827 Coordinates out of bounds (-1) Warning: Frame 29829 Coordinates out of bounds (-1) Warning: Frame 29830 Coordinates out of bounds (-1) Warning: Frame 29831 Coordinates out of bounds (-1) Warning: Frame 29837 Coordinates out of bounds (-1) Warning: Frame 29839 Coordinates out of bounds (-1) Warning: Frame 29860 Coordinates out of bounds (-1) Warning: Frame 29881 Coordinates out of bounds (-1) Warning: Frame 29884 Coordinates out of bounds (-1) Warning: Frame 29888 Coordinates out of bounds (-1) Warning: Frame 29889 Coordinates out of bounds (-1) Warning: Frame 29910 Coordinates out of bounds (-1) Warning: Frame 29949 Coordinates out of bounds (-1) Warning: Frame 29950 Coordinates out of bounds (-1) Warning: Frame 29954 Coordinates out of bounds (-1) Warning: Frame 29955 Coordinates out of bounds (-1) Warning: Frame 29956 Coordinates out of bounds (-1) Warning: Frame 29969 Coordinates out of bounds (-1) Warning: Frame 30084 Coordinates out of bounds (-1) Warning: Frame 30085 Coordinates out of bounds (-1) Warning: Frame 30159 Coordinates out of bounds (-1) Warning: Frame 30160 Coordinates out of bounds (-1) Warning: Frame 30161 Coordinates out of bounds (-1) Warning: Frame 30164 Coordinates out of bounds (-1) Warning: Frame 30167 Coordinates out of bounds (-1) Warning: Frame 30169 Coordinates out of bounds (-1) Warning: Frame 30203 Coordinates out of bounds (-1) Warning: Frame 30224 Coordinates out of bounds (-1) Warning: Frame 30225 Coordinates out of bounds (-1) Warning: Frame 30226 Coordinates out of bounds (-1) Warning: Frame 30227 Coordinates out of bounds (-1) Warning: Frame 30230 Coordinates out of bounds (-1) Warning: Frame 30236 Coordinates out of bounds (-1) 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out of bounds (-1) Warning: Frame 31265 Coordinates out of bounds (-1) Warning: Frame 31320 Coordinates out of bounds (-1) Warning: Frame 31326 Coordinates out of bounds (-1) Warning: Frame 31327 Coordinates out of bounds (-1) Warning: Frame 31328 Coordinates out of bounds (-1) Warning: Frame 31348 Coordinates out of bounds (-1) Warning: Frame 31349 Coordinates out of bounds (-1) Warning: Frame 31360 Coordinates out of bounds (-1) Warning: Frame 31365 Coordinates out of bounds (-1) Warning: Frame 31380 Coordinates out of bounds (-1) Warning: Frame 31388 Coordinates out of bounds (-1) Warning: Frame 31442 Coordinates out of bounds (-1) Warning: Frame 31449 Coordinates out of bounds (-1) Warning: Frame 31460 Coordinates out of bounds (-1) Warning: Frame 31470 Coordinates out of bounds (-1) Warning: Frame 31488 Coordinates out of bounds (-1) Warning: Frame 31580 Coordinates out of bounds (-1) Warning: Frame 31644 Coordinates out of bounds (-1) Warning: Frame 31684 Coordinates out of bounds (-1) Warning: Frame 31685 Coordinates out of bounds (-1) Warning: Frame 31687 Coordinates out of bounds (-1) Warning: Frame 31705 Coordinates out of bounds (-1) Warning: Frame 31724 Coordinates out of bounds (-1) Warning: Frame 31735 Coordinates out of bounds (-1) Warning: Frame 31751 Coordinates out of bounds (-1) Warning: Frame 31768 Coordinates out of bounds (-1) Warning: Frame 31776 Coordinates out of bounds (-1) Warning: Frame 31804 Coordinates out of bounds (-1) Warning: Frame 31840 Coordinates out of bounds (-1) Warning: Frame 31844 Coordinates out of bounds (-1) Warning: Frame 31860 Coordinates out of bounds (-1) Warning: Frame 31914 Coordinates out of bounds (-1) Warning: Frame 31942 Coordinates out of bounds (-1) Warning: Frame 31972 Coordinates out of bounds (-1) Warning: Frame 31983 Coordinates out of bounds (-1) Warning: Frame 31985 Coordinates out of bounds (-1) Warning: Frame 32012 Coordinates out of bounds (-1) Warning: Frame 32054 Coordinates out of bounds (-1) 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Coordinates out of bounds (-1) Warning: Frame 32508 Coordinates out of bounds (-1) Warning: Frame 32544 Coordinates out of bounds (-1) Warning: Frame 32545 Coordinates out of bounds (-1) Warning: Frame 32546 Coordinates out of bounds (-1) Warning: Frame 32549 Coordinates out of bounds (-1) Warning: Frame 32550 Coordinates out of bounds (-1) Warning: Frame 32565 Coordinates out of bounds (-1) Warning: Frame 32568 Coordinates out of bounds (-1) Warning: Frame 32585 Coordinates out of bounds (-1) Warning: Frame 32586 Coordinates out of bounds (-1) Warning: Frame 32601 Coordinates out of bounds (-1) Warning: Frame 32602 Coordinates out of bounds (-1) Warning: Frame 32633 Coordinates out of bounds (-1) Warning: Frame 32646 Coordinates out of bounds (-1) Warning: Frame 32765 Coordinates out of bounds (-1) Warning: Frame 32807 Coordinates out of bounds (-1) Warning: Frame 32814 Coordinates out of bounds (-1) Warning: Frame 32840 Coordinates out of bounds (-1) Warning: Frame 32841 Coordinates out of bounds (-1) Warning: Frame 32849 Coordinates out of bounds (-1) Warning: Frame 32850 Coordinates out of bounds (-1) Warning: Frame 32851 Coordinates out of bounds (-1) Warning: Frame 32911 Coordinates out of bounds (-1) Warning: Frame 32912 Coordinates out of bounds (-1) Warning: Frame 32913 Coordinates out of bounds (-1) Warning: Frame 32924 Coordinates out of bounds (-1) Warning: Frame 32930 Coordinates out of bounds (-1) Warning: Frame 32931 Coordinates out of bounds (-1) Warning: Frame 32986 Coordinates out of bounds (-1) Warning: Frame 33028 Coordinates out of bounds (-1) Warning: Frame 33030 Coordinates out of bounds (-1) Warning: Frame 33031 Coordinates out of bounds (-1) Warning: Frame 33032 Coordinates out of bounds (-1) Warning: Frame 33034 Coordinates out of bounds (-1) Warning: Frame 33035 Coordinates out of bounds (-1) Warning: Frame 33068 Coordinates out of bounds (-1) Warning: Frame 33088 Coordinates out of bounds (-1) Warning: Frame 33090 Coordinates out of bounds (-1) Warning: Frame 33120 Coordinates out of bounds (-1) Warning: Frame 33175 Coordinates out of bounds (-1) Warning: Frame 33197 Coordinates out of bounds (-1) Warning: Frame 33231 Coordinates out of bounds (-1) Warning: Frame 33232 Coordinates out of bounds (-1) Warning: Frame 33237 Coordinates out of bounds (-1) Warning: Frame 33242 Coordinates out of bounds (-1) Warning: Frame 33252 Coordinates out of bounds (-1) Warning: Frame 33256 Coordinates out of bounds (-1) Warning: Frame 33257 Coordinates out of bounds (-1) Warning: Frame 33292 Coordinates out of bounds (-1) Warning: Frame 33316 Coordinates out of bounds (-1) Warning: Frame 33342 Coordinates out of bounds (-1) Warning: Frame 33345 Coordinates out of bounds (-1) Warning: Frame 33346 Coordinates out of bounds (-1) Warning: Frame 33356 Coordinates out of bounds (-1) Warning: Frame 33434 Coordinates out of bounds (-1) Warning: Frame 33439 Coordinates out of bounds (-1) Warning: Frame 33465 Coordinates out of bounds (-1) 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out of bounds (-1) Warning: Frame 34332 Coordinates out of bounds (-1) Warning: Frame 34344 Coordinates out of bounds (-1) Warning: Frame 34363 Coordinates out of bounds (-1) Warning: Frame 34404 Coordinates out of bounds (-1) Warning: Frame 34405 Coordinates out of bounds (-1) Warning: Frame 34406 Coordinates out of bounds (-1) Warning: Frame 34422 Coordinates out of bounds (-1) Warning: Frame 34491 Coordinates out of bounds (-1) Warning: Frame 34515 Coordinates out of bounds (-1) Warning: Frame 34517 Coordinates out of bounds (-1) Warning: Frame 34519 Coordinates out of bounds (-1) Warning: Frame 34522 Coordinates out of bounds (-1) Warning: Frame 34525 Coordinates out of bounds (-1) Warning: Frame 34526 Coordinates out of bounds (-1) Warning: Frame 34529 Coordinates out of bounds (-1) Warning: Frame 34534 Coordinates out of bounds (-1) Warning: Frame 34536 Coordinates out of bounds (-1) Warning: Frame 34538 Coordinates out of bounds (-1) Warning: Frame 34540 Coordinates out of bounds (-1) Warning: Frame 34550 Coordinates out of bounds (-1) Warning: Frame 34584 Coordinates out of bounds (-1) Warning: Frame 34597 Coordinates out of bounds (-1) Warning: Frame 34598 Coordinates out of bounds (-1) Warning: Frame 34617 Coordinates out of bounds (-1) Warning: Frame 34627 Coordinates out of bounds (-1) Warning: Frame 34635 Coordinates out of bounds (-1) Warning: Frame 34637 Coordinates out of bounds (-1) Warning: Frame 34667 Coordinates out of bounds (-1) Warning: Frame 34668 Coordinates out of bounds (-1) Warning: Frame 34683 Coordinates out of bounds (-1) Warning: Frame 34685 Coordinates out of bounds (-1) Warning: Frame 34687 Coordinates out of bounds (-1) Warning: Frame 34718 Coordinates out of bounds (-1) Warning: Frame 34720 Coordinates out of bounds (-1) Warning: Frame 34721 Coordinates out of bounds (-1) Warning: Frame 34722 Coordinates out of bounds (-1) Warning: Frame 34774 Coordinates out of bounds (-1) Warning: Frame 34784 Coordinates out of bounds (-1) 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out of bounds (-1) Warning: Frame 35922 Coordinates out of bounds (-1) Warning: Frame 35923 Coordinates out of bounds (-1) Warning: Frame 35935 Coordinates out of bounds (-1) Warning: Frame 35936 Coordinates out of bounds (-1) Warning: Frame 35938 Coordinates out of bounds (-1) Warning: Frame 35942 Coordinates out of bounds (-1) Warning: Frame 35955 Coordinates out of bounds (-1) Warning: Frame 35956 Coordinates out of bounds (-1) Warning: Frame 35994 Coordinates out of bounds (-1) Warning: Frame 36012 Coordinates out of bounds (-1) Warning: Frame 36028 Coordinates out of bounds (-1) Warning: Frame 36032 Coordinates out of bounds (-1) Warning: Frame 36074 Coordinates out of bounds (-1) Warning: Frame 36111 Coordinates out of bounds (-1) Warning: Frame 36118 Coordinates out of bounds (-1) Warning: Frame 36124 Coordinates out of bounds (-1) Warning: Frame 36125 Coordinates out of bounds (-1) Warning: Frame 36142 Coordinates out of bounds (-1) Warning: Frame 36143 Coordinates out of bounds (-1) Warning: Frame 36149 Coordinates out of bounds (-1) Warning: Frame 36161 Coordinates out of bounds (-1) Warning: Frame 36171 Coordinates out of bounds (-1) Warning: Frame 36225 Coordinates out of bounds (-1) Warning: Frame 36226 Coordinates out of bounds (-1) Warning: Frame 36235 Coordinates out of bounds (-1) Warning: Frame 36237 Coordinates out of bounds (-1) Warning: Frame 36238 Coordinates out of bounds (-1) Warning: Frame 36269 Coordinates out of bounds (-1) Warning: Frame 36270 Coordinates out of bounds (-1) Warning: Frame 36282 Coordinates out of bounds (-1) Warning: Frame 36283 Coordinates out of bounds (-1) Warning: Frame 36284 Coordinates out of bounds (-1) Warning: Frame 36294 Coordinates out of bounds (-1) Warning: Frame 36295 Coordinates out of bounds (-1) Warning: Frame 36301 Coordinates out of bounds (-1) Warning: Frame 36304 Coordinates out of bounds (-1) Warning: Frame 36305 Coordinates out of bounds (-1) Warning: Frame 36345 Coordinates out of bounds (-1) 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out of bounds (-1) Warning: Frame 69543 Coordinates out of bounds (-1) Warning: Frame 69951 Coordinates out of bounds (-1) Warning: Frame 69952 Coordinates out of bounds (-1) Warning: Frame 70472 Coordinates out of bounds (-1) Warning: Frame 70473 Coordinates out of bounds (-1) Warning: Frame 70763 Coordinates out of bounds (-1) Warning: Frame 70764 Coordinates out of bounds (-1) Warning: Frame 70765 Coordinates out of bounds (-1) Warning: Frame 70952 Coordinates out of bounds (-1) Warning: Frame 70953 Coordinates out of bounds (-1) Warning: Frame 70956 Coordinates out of bounds (-1) Warning: Frame 70957 Coordinates out of bounds (-1) Warning: Frame 70958 Coordinates out of bounds (-1) Warning: Frame 70960 Coordinates out of bounds (-1) Warning: Frame 70962 Coordinates out of bounds (-1) Warning: Frame 70964 Coordinates out of bounds (-1) Warning: Frame 70992 Coordinates out of bounds (-1) Warning: Frame 71060 Coordinates out of bounds (-1) Warning: Frame 71061 Coordinates out of bounds (-1) Warning: Frame 71093 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 69979 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 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: 71210 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 71210 TIME: Analyses took 0.0121 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 71210 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 71210 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 71210 COM "COM" (double, distance), size is 71210 g1 "g1" (double, torsion(gamma)), size is 71210 d1 "d1" (double, torsion(delta)), size is 71210 e1 "e1" (double, torsion(epsilon)), size is 71210 z1 "z1" (double, torsion(zeta)), size is 71210 c1 "c1" (double, torsion(chin)), size is 71210 a2 "a2" (double, torsion(alpha)), size is 71210 b2 "b2" (double, torsion(beta)), size is 71210 g2 "g2" (double, torsion(gamma)), size is 71210 d2 "d2" (double, torsion(delta)), size is 71210 c2 "c2" (double, torsion(chin)), size is 71210 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 ( 0.03%) TIME: Trajectory Process : 0.0738 s ( 34.23%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0121 s ( 5.62%) TIME: Data File Write : 0.1296 s ( 60.11%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2155 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.7801 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.