CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:16:38 | Available memory: 2.022 GB INPUT: Reading input from 'pt-analysis1.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c0] Reading '../ctraj.c0' as Amber NetCDF [reference ../../../A-form.pdb [a-form]] Reading '../../../A-form.pdb' as PDB Setting active reference for distance-based masks: 'A-form.pdb' [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [distance dist_sugar_ox :1@O2' :2@O4'] DISTANCE: :1@O2' to :2@O4', center of mass. [distance dist_N3-O5p :1@N3 :1@O5'] DISTANCE: :1@N3 to :1@O5', center of mass. [distance COM :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 (1 total): 0: noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 352470 of 352470) Coordinate processing will occur on 352470 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] Target mask: [:1,2&!@H*](37) Reference mask: [:1,2&!@H*](37) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 1: [distance dist_sugar_ox :1@O2' :2@O4'] :1@O2' (1 atoms) to :2@O4' (1 atoms), imaged. 2: [distance dist_N3-O5p :1@N3 :1@O5'] :1@N3 (1 atoms) to :1@O5' (1 atoms), imaged. 3: [distance COM :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 (1-352470, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 352470 frames and processed 352470 frames. TIME: Avg. throughput= 194595.5794 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 352470 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 352470 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 352470 COM "COM" (double, distance), size is 352470 g1 "g1" (double, torsion(gamma)), size is 352470 d1 "d1" (double, torsion(delta)), size is 352470 e1 "e1" (double, torsion(epsilon)), size is 352470 z1 "z1" (double, torsion(zeta)), size is 352470 c1 "c1" (double, torsion(chin)), size is 352470 a2 "a2" (double, torsion(alpha)), size is 352470 b2 "b2" (double, torsion(beta)), size is 352470 g2 "g2" (double, torsion(gamma)), size is 352470 d2 "d2" (double, torsion(delta)), size is 352470 c2 "c2" (double, torsion(chin)), size is 352470 RUN TIMING: TIME: Init : 0.0049 s ( 0.27%) TIME: Trajectory Process : 1.8113 s ( 99.73%) 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 1.8163 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, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 352470 of 352470) Coordinate processing will occur on 352470 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c0 (1-352470, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 352470 frames and processed 352470 frames. TIME: Avg. throughput= 1027294.8514 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: 352470 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 352470 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: 352470 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 6 Coordinates out of bounds (-1) Warning: Frame 43 Coordinates out of bounds (-1) Warning: Frame 225 Coordinates out of bounds (-1) Warning: Frame 228 Coordinates out of bounds (-1) Warning: Frame 260 Coordinates out of bounds (-1) Warning: Frame 262 Coordinates out of bounds (-1) Warning: Frame 580 Coordinates out of bounds (-1) Warning: Frame 889 Coordinates out of bounds (-1) Warning: Frame 1246 Coordinates out of bounds (-1) Warning: Frame 1882 Coordinates out of bounds (-1) Warning: Frame 2014 Coordinates out of bounds (-1) Warning: Frame 3990 Coordinates out of bounds (-1) Warning: Frame 4459 Coordinates out of bounds (-1) Warning: Frame 4958 Coordinates out of bounds (-1) Warning: Frame 4964 Coordinates out of bounds (-1) Warning: Frame 4965 Coordinates out of bounds (-1) Warning: Frame 4977 Coordinates out of bounds (-1) Warning: Frame 4978 Coordinates out of bounds (-1) Warning: Frame 5296 Coordinates out of bounds (-1) Warning: Frame 6029 Coordinates out of bounds (-1) Warning: Frame 6041 Coordinates out of bounds (-1) Warning: Frame 6232 Coordinates out of bounds (-1) Warning: Frame 6632 Coordinates out of bounds (-1) Warning: Frame 7329 Coordinates out of bounds (-1) Warning: Frame 7330 Coordinates out of bounds (-1) Warning: Frame 8343 Coordinates out of bounds (-1) Warning: Frame 8512 Coordinates out of bounds (-1) Warning: Frame 8514 Coordinates out of bounds (-1) Warning: Frame 8541 Coordinates out of bounds (-1) Warning: Frame 8542 Coordinates out of bounds (-1) Warning: Frame 8632 Coordinates out of bounds (-1) Warning: Frame 9475 Coordinates out of bounds (-1) Warning: Frame 9476 Coordinates out of bounds (-1) Warning: Frame 9477 Coordinates out of bounds (-1) Warning: Frame 9479 Coordinates out of bounds (-1) Warning: Frame 9482 Coordinates out of bounds (-1) Warning: Frame 9659 Coordinates out of bounds (-1) Warning: Frame 9985 Coordinates out of bounds (-1) Warning: Frame 10249 Coordinates out of bounds (-1) Warning: Frame 10253 Coordinates out of bounds (-1) Warning: Frame 10777 Coordinates out of bounds (-1) Warning: Frame 10951 Coordinates out of bounds (-1) Warning: Frame 10986 Coordinates out of bounds (-1) Warning: Frame 11546 Coordinates out of bounds (-1) Warning: Frame 11762 Coordinates out of bounds (-1) Warning: Frame 12163 Coordinates out of bounds (-1) Warning: Frame 12166 Coordinates out of bounds (-1) Warning: Frame 12379 Coordinates out of bounds (-1) Warning: Frame 13326 Coordinates out of bounds (-1) Warning: Frame 13425 Coordinates out of bounds (-1) Warning: Frame 13946 Coordinates out of bounds (-1) Warning: Frame 14206 Coordinates out of bounds (-1) Warning: Frame 14744 Coordinates out of bounds (-1) Warning: Frame 14760 Coordinates out of bounds (-1) Warning: Frame 14886 Coordinates out of bounds (-1) Warning: Frame 15007 Coordinates out of bounds (-1) Warning: Frame 15010 Coordinates out of bounds (-1) Warning: Frame 15689 Coordinates out of bounds (-1) Warning: Frame 17174 Coordinates out of bounds (-1) Warning: Frame 17885 Coordinates out of bounds (-1) Warning: Frame 18901 Coordinates out of bounds (-1) Warning: Frame 18911 Coordinates out of bounds (-1) Warning: Frame 19084 Coordinates out of bounds (-1) Warning: Frame 19431 Coordinates out of bounds (-1) Warning: Frame 19884 Coordinates out of bounds (-1) Warning: Frame 19891 Coordinates out of bounds (-1) Warning: Frame 19900 Coordinates out of bounds (-1) Warning: Frame 19901 Coordinates out of bounds (-1) Warning: Frame 20280 Coordinates out of bounds (-1) Warning: Frame 20355 Coordinates out of bounds (-1) Warning: Frame 20479 Coordinates out of bounds (-1) Warning: Frame 20546 Coordinates out of bounds (-1) Warning: Frame 20555 Coordinates out of bounds (-1) Warning: Frame 21188 Coordinates out of bounds (-1) Warning: Frame 21272 Coordinates out of bounds (-1) Warning: Frame 21273 Coordinates out of bounds (-1) Warning: Frame 21274 Coordinates out of bounds (-1) Warning: Frame 21275 Coordinates out of bounds (-1) Warning: Frame 22190 Coordinates out of bounds (-1) Warning: Frame 22192 Coordinates out of bounds (-1) Warning: Frame 22193 Coordinates out of bounds (-1) Warning: Frame 22981 Coordinates out of bounds (-1) Warning: Frame 23464 Coordinates out of bounds (-1) Warning: Frame 23550 Coordinates out of bounds (-1) Warning: Frame 24041 Coordinates out of bounds (-1) Warning: Frame 24271 Coordinates out of bounds (-1) Warning: Frame 24691 Coordinates out of bounds (-1) Warning: Frame 24696 Coordinates out of bounds (-1) Warning: Frame 25200 Coordinates out of bounds (-1) Warning: Frame 26048 Coordinates out of bounds (-1) Warning: Frame 26791 Coordinates out of bounds (-1) Warning: Frame 27069 Coordinates out of bounds (-1) Warning: Frame 27455 Coordinates out of bounds (-1) Warning: Frame 27457 Coordinates out of bounds (-1) Warning: Frame 27911 Coordinates out of bounds (-1) Warning: Frame 27944 Coordinates out of bounds (-1) Warning: Frame 27945 Coordinates out of bounds (-1) Warning: Frame 27949 Coordinates out of bounds (-1) Warning: Frame 28312 Coordinates out of bounds (-1) Warning: Frame 28314 Coordinates out of bounds (-1) Warning: Frame 28317 Coordinates out of bounds (-1) Warning: Frame 28319 Coordinates out of bounds (-1) Warning: Frame 29842 Coordinates out of bounds (-1) Warning: Frame 30430 Coordinates out of bounds (-1) Warning: Frame 30433 Coordinates out of bounds (-1) Warning: Frame 31665 Coordinates out of bounds (-1) Warning: Frame 31942 Coordinates out of bounds (-1) Warning: Frame 32538 Coordinates out of bounds (-1) Warning: Frame 32539 Coordinates out of bounds (-1) Warning: Frame 32804 Coordinates out of bounds (-1) Warning: Frame 34165 Coordinates out of bounds (-1) Warning: Frame 34203 Coordinates out of bounds (-1) Warning: Frame 34204 Coordinates out of bounds (-1) Warning: Frame 34683 Coordinates out of bounds (-1) Warning: Frame 34703 Coordinates out of bounds (-1) Warning: Frame 34706 Coordinates out of bounds (-1) Warning: Frame 34739 Coordinates out of bounds (-1) Warning: Frame 34741 Coordinates out of bounds (-1) Warning: Frame 34827 Coordinates out of bounds (-1) Warning: Frame 34842 Coordinates out of bounds (-1) Warning: Frame 34843 Coordinates out of bounds (-1) Warning: Frame 34848 Coordinates out of bounds (-1) Warning: Frame 34935 Coordinates out of bounds (-1) Warning: Frame 35167 Coordinates out of bounds (-1) Warning: Frame 35269 Coordinates out of bounds (-1) Warning: Frame 36148 Coordinates out of bounds (-1) Warning: Frame 36180 Coordinates out of bounds (-1) Warning: Frame 36645 Coordinates out of bounds (-1) Warning: Frame 36864 Coordinates out of bounds (-1) Warning: Frame 36866 Coordinates out of bounds (-1) Warning: Frame 36870 Coordinates out of bounds (-1) Warning: Frame 36872 Coordinates out of bounds (-1) Warning: Frame 37002 Coordinates out of bounds (-1) Warning: Frame 37350 Coordinates out of bounds (-1) Warning: Frame 38185 Coordinates out of bounds (-1) Warning: Frame 38661 Coordinates out of bounds (-1) Warning: Frame 38662 Coordinates out of bounds (-1) Warning: Frame 39179 Coordinates out of bounds (-1) Warning: Frame 39180 Coordinates out of bounds (-1) Warning: Frame 39234 Coordinates out of bounds (-1) Warning: Frame 39250 Coordinates out of bounds (-1) Warning: Frame 40495 Coordinates out of bounds (-1) Warning: Frame 41009 Coordinates out of bounds (-1) Warning: Frame 41010 Coordinates out of bounds (-1) Warning: Frame 41014 Coordinates out of bounds (-1) Warning: Frame 41018 Coordinates out of bounds (-1) Warning: Frame 41962 Coordinates out of bounds (-1) Warning: Frame 42395 Coordinates out of bounds (-1) Warning: Frame 42398 Coordinates out of bounds (-1) Warning: Frame 42660 Coordinates out of bounds (-1) Warning: Frame 42718 Coordinates out of bounds (-1) Warning: Frame 42926 Coordinates out of bounds (-1) Warning: Frame 43638 Coordinates out of bounds (-1) Warning: Frame 43862 Coordinates out of bounds (-1) Warning: Frame 44133 Coordinates out of bounds (-1) Warning: Frame 44176 Coordinates out of bounds (-1) Warning: Frame 44179 Coordinates out of bounds (-1) Warning: Frame 44180 Coordinates out of bounds (-1) Warning: Frame 44257 Coordinates out of bounds (-1) Warning: Frame 44869 Coordinates out of bounds (-1) Warning: Frame 46333 Coordinates out of bounds (-1) Warning: Frame 46336 Coordinates out of bounds (-1) Warning: Frame 46343 Coordinates out of bounds (-1) Warning: Frame 46344 Coordinates out of bounds (-1) Warning: Frame 46359 Coordinates out of bounds (-1) Warning: Frame 47021 Coordinates out of bounds (-1) Warning: Frame 47481 Coordinates out of bounds (-1) Warning: Frame 48489 Coordinates out of bounds (-1) Warning: Frame 48554 Coordinates out of bounds (-1) Warning: Frame 48555 Coordinates out of bounds (-1) Warning: Frame 48556 Coordinates out of bounds (-1) Warning: Frame 48623 Coordinates out of bounds (-1) Warning: Frame 48739 Coordinates out of bounds (-1) Warning: Frame 48824 Coordinates out of bounds (-1) Warning: Frame 48827 Coordinates out of bounds (-1) Warning: Frame 49038 Coordinates out of bounds (-1) Warning: Frame 49552 Coordinates out of bounds (-1) Warning: Frame 50224 Coordinates out of bounds (-1) Warning: Frame 50620 Coordinates out of bounds (-1) Warning: Frame 50764 Coordinates out of bounds (-1) Warning: Frame 50765 Coordinates out of bounds (-1) Warning: Frame 51111 Coordinates out of bounds (-1) Warning: Frame 51112 Coordinates out of bounds (-1) Warning: Frame 51438 Coordinates out of bounds (-1) Warning: Frame 51628 Coordinates out of bounds (-1) Warning: Frame 51629 Coordinates out of bounds (-1) Warning: Frame 51922 Coordinates out of bounds (-1) Warning: Frame 51923 Coordinates out of bounds (-1) Warning: Frame 52329 Coordinates out of bounds (-1) Warning: Frame 52433 Coordinates out of bounds (-1) Warning: Frame 52434 Coordinates out of bounds (-1) Warning: Frame 52589 Coordinates out of bounds (-1) Warning: Frame 53384 Coordinates out of bounds (-1) Warning: Frame 53408 Coordinates out of bounds (-1) Warning: Frame 53409 Coordinates out of bounds (-1) Warning: Frame 53862 Coordinates out of bounds (-1) Warning: Frame 54149 Coordinates out of bounds (-1) Warning: Frame 54226 Coordinates out of bounds (-1) Warning: Frame 54228 Coordinates out of bounds (-1) Warning: Frame 54716 Coordinates out of bounds (-1) Warning: Frame 54748 Coordinates out of bounds (-1) Warning: Frame 55054 Coordinates out of bounds (-1) Warning: Frame 55432 Coordinates out of bounds (-1) Warning: Frame 55488 Coordinates out of bounds (-1) Warning: Frame 56245 Coordinates out of bounds (-1) Warning: Frame 56620 Coordinates out of bounds (-1) Warning: Frame 56999 Coordinates out of bounds (-1) Warning: Frame 57083 Coordinates out of bounds (-1) Warning: Frame 57084 Coordinates out of bounds (-1) Warning: Frame 58116 Coordinates out of bounds (-1) Warning: Frame 58117 Coordinates out of bounds (-1) Warning: Frame 58121 Coordinates out of bounds (-1) Warning: Frame 60569 Coordinates out of bounds (-1) Warning: Frame 61451 Coordinates out of bounds (-1) Warning: Frame 61867 Coordinates out of bounds (-1) Warning: Frame 62006 Coordinates out of bounds (-1) Warning: Frame 63106 Coordinates out of bounds (-1) Warning: Frame 63750 Coordinates out of bounds (-1) Warning: Frame 63751 Coordinates out of bounds (-1) Warning: Frame 64411 Coordinates out of bounds (-1) Warning: Frame 64721 Coordinates out of bounds (-1) Warning: Frame 64923 Coordinates out of bounds (-1) Warning: Frame 65270 Coordinates out of bounds (-1) Warning: Frame 66088 Coordinates out of bounds (-1) Warning: Frame 66977 Coordinates out of bounds (-1) Warning: Frame 67050 Coordinates out of bounds (-1) Warning: Frame 67053 Coordinates out of bounds (-1) Warning: Frame 67276 Coordinates out of bounds (-1) Warning: Frame 67370 Coordinates out of bounds (-1) Warning: Frame 69127 Coordinates out of bounds (-1) Warning: Frame 69321 Coordinates out of bounds (-1) Warning: Frame 69348 Coordinates out of bounds (-1) Warning: Frame 69582 Coordinates out of bounds (-1) Warning: Frame 69585 Coordinates out of bounds (-1) Warning: Frame 69586 Coordinates out of bounds (-1) Warning: Frame 69732 Coordinates out of bounds (-1) Warning: Frame 69980 Coordinates out of bounds (-1) Warning: Frame 69992 Coordinates out of bounds (-1) Warning: Frame 70028 Coordinates out of bounds (-1) Warning: Frame 70101 Coordinates out of bounds (-1) Warning: Frame 70694 Coordinates out of bounds (-1) Warning: Frame 71311 Coordinates out of bounds (-1) Warning: Frame 72234 Coordinates out of bounds (-1) Warning: Frame 72402 Coordinates out of bounds (-1) Warning: Frame 72694 Coordinates out of bounds (-1) Warning: Frame 72766 Coordinates out of bounds (-1) Warning: Frame 72767 Coordinates out of bounds (-1) Warning: Frame 72807 Coordinates out of bounds (-1) Warning: Frame 72809 Coordinates out of bounds (-1) Warning: Frame 72811 Coordinates out of bounds (-1) Warning: Frame 73386 Coordinates out of bounds (-1) Warning: Frame 73555 Coordinates out of bounds (-1) Warning: Frame 73556 Coordinates out of bounds (-1) Warning: Frame 74271 Coordinates out of bounds (-1) Warning: Frame 74422 Coordinates out of bounds (-1) Warning: Frame 74423 Coordinates out of bounds (-1) Warning: Frame 74745 Coordinates out of bounds (-1) Warning: Frame 76169 Coordinates out of bounds (-1) Warning: Frame 76736 Coordinates out of bounds (-1) Warning: Frame 77584 Coordinates out of bounds (-1) Warning: Frame 77827 Coordinates out of bounds (-1) Warning: Frame 77833 Coordinates out of bounds (-1) Warning: Frame 77834 Coordinates out of bounds (-1) Warning: Frame 77963 Coordinates out of bounds (-1) Warning: Frame 78209 Coordinates out of bounds (-1) Warning: Frame 78218 Coordinates out of bounds (-1) Warning: Frame 78219 Coordinates out of bounds (-1) Warning: Frame 78220 Coordinates out of bounds (-1) Warning: Frame 78221 Coordinates out of 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out of bounds (-1) Warning: Frame 133879 Coordinates out of bounds (-1) Warning: Frame 135168 Coordinates out of bounds (-1) Warning: Frame 135359 Coordinates out of bounds (-1) Warning: Frame 136118 Coordinates out of bounds (-1) Warning: Frame 136836 Coordinates out of bounds (-1) Warning: Frame 136883 Coordinates out of bounds (-1) Warning: Frame 136930 Coordinates out of bounds (-1) Warning: Frame 137173 Coordinates out of bounds (-1) Warning: Frame 137245 Coordinates out of bounds (-1) Warning: Frame 138131 Coordinates out of bounds (-1) Warning: Frame 139215 Coordinates out of bounds (-1) Warning: Frame 139220 Coordinates out of bounds (-1) Warning: Frame 140198 Coordinates out of bounds (-1) Warning: Frame 140701 Coordinates out of bounds (-1) Warning: Frame 140702 Coordinates out of bounds (-1) Warning: Frame 140821 Coordinates out of bounds (-1) Warning: Frame 140907 Coordinates out of bounds (-1) Warning: Frame 141514 Coordinates out of bounds (-1) Warning: Frame 141516 Coordinates out of bounds (-1) Warning: Frame 141517 Coordinates out of bounds (-1) Warning: Frame 141654 Coordinates out of bounds (-1) Warning: Frame 142168 Coordinates out of bounds (-1) Warning: Frame 142169 Coordinates out of bounds (-1) Warning: Frame 142413 Coordinates out of bounds (-1) Warning: Frame 142414 Coordinates out of bounds (-1) Warning: Frame 142417 Coordinates out of bounds (-1) Warning: Frame 142836 Coordinates out of bounds (-1) Warning: Frame 142863 Coordinates out of bounds (-1) Warning: Frame 142889 Coordinates out of bounds (-1) Warning: Frame 142893 Coordinates out of bounds (-1) Warning: Frame 142926 Coordinates out of bounds (-1) Warning: Frame 143084 Coordinates out of bounds (-1) Warning: Frame 143481 Coordinates out of bounds (-1) Warning: Frame 143569 Coordinates out of bounds (-1) Warning: Frame 143637 Coordinates out of bounds (-1) Warning: Frame 143762 Coordinates out of bounds (-1) Warning: Frame 143778 Coordinates out of bounds (-1) Warning: Frame 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bounds (-1) Warning: Frame 153612 Coordinates out of bounds (-1) Warning: Frame 153742 Coordinates out of bounds (-1) Warning: Frame 154095 Coordinates out of bounds (-1) Warning: Frame 154178 Coordinates out of bounds (-1) Warning: Frame 154181 Coordinates out of bounds (-1) Warning: Frame 154409 Coordinates out of bounds (-1) Warning: Frame 154427 Coordinates out of bounds (-1) Warning: Frame 154454 Coordinates out of bounds (-1) Warning: Frame 154455 Coordinates out of bounds (-1) Warning: Frame 154642 Coordinates out of bounds (-1) Warning: Frame 154644 Coordinates out of bounds (-1) Warning: Frame 154692 Coordinates out of bounds (-1) Warning: Frame 154770 Coordinates out of bounds (-1) Warning: Frame 154771 Coordinates out of bounds (-1) Warning: Frame 154779 Coordinates out of bounds (-1) Warning: Frame 154818 Coordinates out of bounds (-1) Warning: Frame 155101 Coordinates out of bounds (-1) Warning: Frame 155136 Coordinates out of bounds (-1) Warning: Frame 155774 Coordinates out of bounds (-1) Warning: Frame 156235 Coordinates out of bounds (-1) Warning: Frame 156643 Coordinates out of bounds (-1) Warning: Frame 157644 Coordinates out of bounds (-1) Warning: Frame 157645 Coordinates out of bounds (-1) Warning: Frame 157669 Coordinates out of bounds (-1) Warning: Frame 157903 Coordinates out of bounds (-1) Warning: Frame 157904 Coordinates out of bounds (-1) Warning: Frame 158429 Coordinates out of bounds (-1) Warning: Frame 158737 Coordinates out of bounds (-1) Warning: Frame 158994 Coordinates out of bounds (-1) Warning: Frame 159102 Coordinates out of bounds (-1) Warning: Frame 159680 Coordinates out of bounds (-1) Warning: Frame 159681 Coordinates out of bounds (-1) Warning: Frame 160277 Coordinates out of bounds (-1) Warning: Frame 160281 Coordinates out of bounds (-1) Warning: Frame 160816 Coordinates out of bounds (-1) Warning: Frame 161627 Coordinates out of bounds (-1) Warning: Frame 161884 Coordinates out of bounds (-1) Warning: Frame 162746 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351165 Coordinates out of bounds (-1) Warning: Frame 351167 Coordinates out of bounds (-1) Warning: Frame 351357 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 350955 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 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: 352470 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 352470 TIME: Analyses took 0.0654 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 352470 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 352470 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 352470 COM "COM" (double, distance), size is 352470 g1 "g1" (double, torsion(gamma)), size is 352470 d1 "d1" (double, torsion(delta)), size is 352470 e1 "e1" (double, torsion(epsilon)), size is 352470 z1 "z1" (double, torsion(zeta)), size is 352470 c1 "c1" (double, torsion(chin)), size is 352470 a2 "a2" (double, torsion(alpha)), size is 352470 b2 "b2" (double, torsion(beta)), size is 352470 g2 "g2" (double, torsion(gamma)), size is 352470 d2 "d2" (double, torsion(delta)), size is 352470 c2 "c2" (double, torsion(chin)), size is 352470 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 : 0.0069 s ( 1.37%) TIME: Trajectory Process : 0.3431 s ( 67.99%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0654 s ( 12.96%) TIME: Data File Write : 0.0892 s ( 17.67%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5047 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2.3313 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.