CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 15:13:54 | Available memory: 2.397 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.c5] Reading '../ctraj.c5' 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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@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@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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2722 of 2722) Coordinate processing will occur on 2722 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 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@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@N1 :2@C2 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c5 (1-2722, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 2722 frames and processed 2722 frames. TIME: Avg. throughput= 102856.7110 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 2722 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 2722 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 2722 COM "COM" (double, distance), size is 2722 g1 "g1" (double, torsion(gamma)), size is 2722 d1 "d1" (double, torsion(delta)), size is 2722 e1 "e1" (double, torsion(epsilon)), size is 2722 z1 "z1" (double, torsion(zeta)), size is 2722 c1 "c1" (double, torsion(chin)), size is 2722 a2 "a2" (double, torsion(alpha)), size is 2722 b2 "b2" (double, torsion(beta)), size is 2722 g2 "g2" (double, torsion(gamma)), size is 2722 d2 "d2" (double, torsion(delta)), size is 2722 c2 "c2" (double, torsion(chin)), size is 2722 RUN TIMING: TIME: Init : 0.0000 s ( 0.18%) TIME: Trajectory Process : 0.0265 s ( 99.57%) TIME: Action Post : 0.0000 s ( 0.02%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.12%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0266 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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2722 of 2722) Coordinate processing will occur on 2722 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c5 (1-2722, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 2722 frames and processed 2722 frames. TIME: Avg. throughput= 382357.0726 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: 2722 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 2722 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: 2722 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 3 Coordinates out of bounds (-1) Warning: Frame 4 Coordinates out of bounds (-1) Warning: Frame 6 Coordinates out of bounds (-1) Warning: Frame 7 Coordinates out of bounds (-1) Warning: Frame 8 Coordinates out of bounds (-1) Warning: Frame 9 Coordinates out of bounds (-1) Warning: Frame 10 Coordinates out of bounds (-1) Warning: Frame 13 Coordinates out of bounds (-1) Warning: Frame 14 Coordinates out of bounds (-1) Warning: Frame 15 Coordinates out of bounds (-1) Warning: Frame 31 Coordinates out of bounds (-1) Warning: Frame 44 Coordinates out of bounds (-1) Warning: Frame 45 Coordinates out of bounds (-1) Warning: Frame 48 Coordinates out of bounds (-1) Warning: Frame 49 Coordinates out of bounds (-1) Warning: Frame 51 Coordinates out of bounds (-1) Warning: Frame 52 Coordinates out of bounds (-1) Warning: Frame 55 Coordinates out of bounds (-1) Warning: Frame 56 Coordinates out of bounds (-1) Warning: Frame 59 Coordinates out of bounds (-1) Warning: Frame 65 Coordinates out of bounds (-1) Warning: Frame 68 Coordinates out of bounds (-1) Warning: Frame 77 Coordinates out of bounds (-1) Warning: Frame 80 Coordinates out of bounds (-1) Warning: Frame 85 Coordinates out of bounds (-1) Warning: Frame 87 Coordinates out of bounds (-1) Warning: Frame 88 Coordinates out of bounds (-1) Warning: Frame 93 Coordinates out of bounds (-1) Warning: Frame 97 Coordinates out of bounds (-1) Warning: Frame 99 Coordinates out of bounds (-1) Warning: Frame 100 Coordinates out of bounds (-1) Warning: Frame 115 Coordinates out of bounds (-1) Warning: Frame 117 Coordinates out of bounds (-1) Warning: Frame 129 Coordinates out of bounds (-1) Warning: Frame 134 Coordinates out of bounds (-1) Warning: Frame 135 Coordinates out of bounds (-1) Warning: Frame 136 Coordinates out of bounds (-1) Warning: Frame 137 Coordinates out of bounds (-1) Warning: Frame 141 Coordinates out of bounds (-1) Warning: Frame 142 Coordinates out of bounds (-1) Warning: Frame 174 Coordinates out of bounds (-1) Warning: Frame 175 Coordinates out of bounds (-1) Warning: Frame 178 Coordinates out of bounds (-1) Warning: Frame 179 Coordinates out of bounds (-1) Warning: Frame 185 Coordinates out of bounds (-1) Warning: Frame 187 Coordinates out of bounds (-1) Warning: Frame 191 Coordinates out of bounds (-1) Warning: Frame 211 Coordinates out of bounds (-1) Warning: Frame 213 Coordinates out of bounds (-1) Warning: Frame 214 Coordinates out of bounds (-1) Warning: Frame 215 Coordinates out of bounds (-1) Warning: Frame 216 Coordinates out of bounds (-1) Warning: Frame 217 Coordinates out of bounds (-1) Warning: Frame 218 Coordinates out of bounds (-1) Warning: Frame 219 Coordinates out of bounds (-1) Warning: Frame 220 Coordinates out of bounds (-1) Warning: Frame 224 Coordinates out of bounds (-1) Warning: Frame 228 Coordinates out of bounds (-1) Warning: Frame 229 Coordinates out of bounds (-1) Warning: Frame 233 Coordinates out of bounds (-1) Warning: Frame 234 Coordinates out of bounds (-1) Warning: Frame 242 Coordinates out of bounds (-1) Warning: Frame 250 Coordinates out of bounds (-1) Warning: Frame 274 Coordinates out of bounds (-1) Warning: Frame 278 Coordinates out of bounds (-1) Warning: Frame 283 Coordinates out of bounds (-1) Warning: Frame 293 Coordinates out of bounds (-1) Warning: Frame 294 Coordinates out of bounds (-1) Warning: Frame 297 Coordinates out of bounds (-1) Warning: Frame 298 Coordinates out of bounds (-1) Warning: Frame 308 Coordinates out of bounds (-1) Warning: Frame 324 Coordinates out of bounds (-1) Warning: Frame 352 Coordinates out of bounds (-1) Warning: Frame 356 Coordinates out of bounds (-1) Warning: Frame 360 Coordinates out of bounds (-1) Warning: Frame 377 Coordinates out of bounds (-1) Warning: Frame 378 Coordinates out of bounds (-1) Warning: Frame 379 Coordinates out of bounds (-1) Warning: Frame 380 Coordinates out of bounds (-1) Warning: Frame 395 Coordinates out of bounds (-1) Warning: Frame 402 Coordinates out of bounds (-1) Warning: Frame 403 Coordinates out of bounds (-1) Warning: Frame 407 Coordinates out of bounds (-1) Warning: Frame 408 Coordinates out of bounds (-1) Warning: Frame 413 Coordinates out of bounds (-1) Warning: Frame 414 Coordinates out of bounds (-1) Warning: Frame 424 Coordinates out of bounds (-1) Warning: Frame 427 Coordinates out of bounds (-1) Warning: Frame 428 Coordinates out of bounds (-1) Warning: Frame 430 Coordinates out of bounds (-1) Warning: Frame 431 Coordinates out of bounds (-1) Warning: Frame 432 Coordinates out of bounds (-1) Warning: Frame 433 Coordinates out of bounds (-1) Warning: Frame 436 Coordinates out of bounds (-1) Warning: Frame 437 Coordinates out of bounds (-1) Warning: Frame 438 Coordinates out of bounds (-1) Warning: Frame 439 Coordinates out of bounds (-1) Warning: Frame 440 Coordinates out of bounds (-1) Warning: Frame 444 Coordinates out of bounds (-1) Warning: Frame 445 Coordinates out of bounds (-1) Warning: Frame 446 Coordinates out of bounds (-1) Warning: Frame 447 Coordinates out of bounds (-1) Warning: Frame 451 Coordinates out of bounds (-1) Warning: Frame 452 Coordinates out of bounds (-1) Warning: Frame 453 Coordinates out of bounds (-1) Warning: Frame 454 Coordinates out of bounds (-1) Warning: Frame 462 Coordinates out of bounds (-1) Warning: Frame 466 Coordinates out of bounds (-1) Warning: Frame 480 Coordinates out of bounds (-1) Warning: Frame 483 Coordinates out of bounds (-1) Warning: Frame 487 Coordinates out of bounds (-1) Warning: Frame 488 Coordinates out of bounds (-1) Warning: Frame 493 Coordinates out of bounds (-1) Warning: Frame 495 Coordinates out of bounds (-1) Warning: Frame 496 Coordinates out of bounds (-1) Warning: Frame 505 Coordinates out of bounds (-1) Warning: Frame 506 Coordinates out of bounds (-1) Warning: Frame 507 Coordinates out of bounds (-1) Warning: Frame 510 Coordinates out of bounds (-1) Warning: Frame 512 Coordinates out of bounds (-1) Warning: Frame 519 Coordinates out of bounds (-1) Warning: Frame 527 Coordinates out of bounds (-1) Warning: Frame 528 Coordinates out of bounds (-1) Warning: Frame 529 Coordinates out of bounds (-1) Warning: Frame 530 Coordinates out of bounds (-1) Warning: Frame 531 Coordinates out of bounds (-1) Warning: Frame 532 Coordinates out of bounds (-1) Warning: Frame 533 Coordinates out of bounds (-1) Warning: Frame 534 Coordinates out of bounds (-1) Warning: Frame 540 Coordinates out of bounds (-1) Warning: Frame 548 Coordinates out of bounds (-1) Warning: Frame 550 Coordinates out of bounds (-1) Warning: Frame 552 Coordinates out of bounds (-1) Warning: Frame 555 Coordinates out of bounds (-1) Warning: Frame 558 Coordinates out of bounds (-1) Warning: Frame 571 Coordinates out of bounds (-1) Warning: Frame 583 Coordinates out of bounds (-1) Warning: Frame 584 Coordinates out of bounds (-1) Warning: Frame 593 Coordinates out of bounds (-1) Warning: Frame 599 Coordinates out of bounds (-1) Warning: Frame 602 Coordinates out of bounds (-1) Warning: Frame 603 Coordinates out of bounds (-1) Warning: Frame 604 Coordinates out of bounds (-1) Warning: Frame 605 Coordinates out of bounds (-1) Warning: Frame 606 Coordinates out of bounds (-1) Warning: Frame 609 Coordinates out of bounds (-1) Warning: Frame 619 Coordinates out of bounds (-1) Warning: Frame 623 Coordinates out of bounds (-1) Warning: Frame 626 Coordinates out of bounds (-1) Warning: Frame 627 Coordinates out of bounds (-1) Warning: Frame 629 Coordinates out of bounds (-1) Warning: Frame 631 Coordinates out of bounds (-1) Warning: Frame 632 Coordinates out of bounds (-1) Warning: Frame 633 Coordinates out of bounds (-1) Warning: Frame 634 Coordinates out of bounds (-1) Warning: Frame 658 Coordinates out of bounds (-1) Warning: Frame 660 Coordinates out of bounds (-1) Warning: Frame 663 Coordinates out of bounds (-1) Warning: Frame 665 Coordinates out of bounds (-1) Warning: Frame 666 Coordinates out of bounds (-1) Warning: Frame 676 Coordinates out of bounds (-1) Warning: Frame 681 Coordinates out of bounds (-1) Warning: Frame 691 Coordinates out of bounds (-1) Warning: Frame 700 Coordinates out of bounds (-1) Warning: Frame 711 Coordinates out of bounds (-1) Warning: Frame 713 Coordinates out of bounds (-1) Warning: Frame 714 Coordinates out of bounds (-1) Warning: Frame 719 Coordinates out of bounds (-1) Warning: Frame 723 Coordinates out of bounds (-1) Warning: Frame 727 Coordinates out of bounds (-1) Warning: Frame 736 Coordinates out of bounds (-1) Warning: Frame 737 Coordinates out of bounds (-1) Warning: Frame 738 Coordinates out of bounds (-1) Warning: Frame 744 Coordinates out of bounds (-1) Warning: Frame 745 Coordinates out of bounds (-1) Warning: Frame 747 Coordinates out of bounds (-1) Warning: Frame 750 Coordinates out of bounds (-1) Warning: Frame 751 Coordinates out of bounds (-1) Warning: Frame 754 Coordinates out of bounds (-1) Warning: Frame 756 Coordinates out of bounds (-1) Warning: Frame 757 Coordinates out of bounds (-1) Warning: Frame 764 Coordinates out of bounds (-1) Warning: Frame 768 Coordinates out of bounds (-1) Warning: Frame 770 Coordinates out of bounds (-1) Warning: Frame 772 Coordinates out of bounds (-1) Warning: Frame 773 Coordinates out of bounds (-1) Warning: Frame 775 Coordinates out of bounds (-1) Warning: Frame 777 Coordinates out of bounds (-1) Warning: Frame 778 Coordinates out of bounds (-1) Warning: Frame 780 Coordinates out of bounds (-1) Warning: Frame 781 Coordinates out of bounds (-1) Warning: Frame 782 Coordinates out of bounds (-1) Warning: Frame 790 Coordinates out of bounds (-1) Warning: Frame 794 Coordinates out of bounds (-1) Warning: Frame 800 Coordinates out of bounds (-1) Warning: Frame 801 Coordinates out of bounds (-1) Warning: Frame 802 Coordinates out of bounds (-1) Warning: Frame 818 Coordinates out of bounds (-1) Warning: Frame 819 Coordinates out of bounds (-1) Warning: Frame 820 Coordinates out of bounds (-1) Warning: Frame 827 Coordinates out of bounds (-1) Warning: Frame 838 Coordinates out of bounds (-1) Warning: Frame 841 Coordinates out of bounds (-1) Warning: Frame 843 Coordinates out of bounds (-1) Warning: Frame 844 Coordinates out of bounds (-1) Warning: Frame 845 Coordinates out of bounds (-1) Warning: Frame 847 Coordinates out of bounds (-1) Warning: Frame 848 Coordinates out of bounds (-1) Warning: Frame 849 Coordinates out of bounds (-1) Warning: Frame 850 Coordinates out of bounds (-1) Warning: Frame 861 Coordinates out of bounds (-1) Warning: Frame 864 Coordinates out of bounds (-1) Warning: Frame 869 Coordinates out of bounds (-1) Warning: Frame 870 Coordinates out of bounds (-1) Warning: Frame 883 Coordinates out of bounds (-1) Warning: Frame 916 Coordinates out of bounds (-1) Warning: Frame 923 Coordinates out of bounds (-1) Warning: Frame 924 Coordinates out of bounds (-1) Warning: Frame 925 Coordinates out of bounds (-1) Warning: Frame 951 Coordinates out of bounds (-1) Warning: Frame 952 Coordinates out of bounds (-1) Warning: Frame 953 Coordinates out of bounds (-1) Warning: Frame 960 Coordinates out of bounds (-1) Warning: Frame 977 Coordinates out of bounds (-1) Warning: Frame 983 Coordinates out of bounds (-1) Warning: Frame 990 Coordinates out of bounds (-1) Warning: Frame 992 Coordinates out of bounds (-1) Warning: Frame 1015 Coordinates out of bounds (-1) Warning: Frame 1016 Coordinates out of bounds (-1) Warning: Frame 1040 Coordinates out of bounds (-1) Warning: Frame 1043 Coordinates out of bounds (-1) Warning: Frame 1044 Coordinates out of bounds (-1) Warning: Frame 1045 Coordinates out of bounds (-1) Warning: Frame 1046 Coordinates out of bounds (-1) Warning: Frame 1060 Coordinates out of bounds (-1) Warning: Frame 1064 Coordinates out of bounds (-1) Warning: Frame 1075 Coordinates out of bounds (-1) Warning: Frame 1076 Coordinates out of bounds (-1) Warning: Frame 1087 Coordinates out of bounds (-1) Warning: Frame 1090 Coordinates out of bounds (-1) Warning: Frame 1091 Coordinates out of bounds (-1) Warning: Frame 1094 Coordinates out of bounds (-1) Warning: Frame 1095 Coordinates out of bounds (-1) Warning: Frame 1102 Coordinates out of bounds (-1) Warning: Frame 1103 Coordinates out of bounds (-1) Warning: Frame 1108 Coordinates out of bounds (-1) Warning: Frame 1109 Coordinates out of bounds (-1) Warning: Frame 1114 Coordinates out of bounds (-1) Warning: Frame 1115 Coordinates out of bounds (-1) Warning: Frame 1116 Coordinates out of bounds (-1) Warning: Frame 1118 Coordinates out of bounds (-1) Warning: Frame 1141 Coordinates out of bounds (-1) Warning: Frame 1143 Coordinates out of bounds (-1) Warning: Frame 1149 Coordinates out of bounds (-1) Warning: Frame 1151 Coordinates out of bounds (-1) Warning: Frame 1205 Coordinates out of bounds (-1) Warning: Frame 1211 Coordinates out of bounds (-1) Warning: Frame 1212 Coordinates out of bounds (-1) Warning: Frame 1213 Coordinates out of bounds (-1) Warning: Frame 1215 Coordinates out of bounds (-1) Warning: Frame 1217 Coordinates out of bounds (-1) Warning: Frame 1218 Coordinates out of bounds (-1) Warning: Frame 1223 Coordinates out of bounds (-1) Warning: Frame 1224 Coordinates out of bounds (-1) Warning: Frame 1233 Coordinates out of bounds (-1) Warning: Frame 1235 Coordinates out of bounds (-1) Warning: Frame 1236 Coordinates out of bounds (-1) Warning: Frame 1240 Coordinates out of bounds (-1) Warning: Frame 1242 Coordinates out of bounds (-1) Warning: Frame 1243 Coordinates out of bounds (-1) Warning: Frame 1245 Coordinates out of bounds (-1) Warning: Frame 1247 Coordinates out of bounds (-1) Warning: Frame 1248 Coordinates out of bounds (-1) Warning: Frame 1249 Coordinates out of bounds (-1) Warning: Frame 1280 Coordinates out of bounds (-1) Warning: Frame 1291 Coordinates out of bounds (-1) Warning: Frame 1304 Coordinates out of bounds (-1) Warning: Frame 1305 Coordinates out of bounds (-1) Warning: Frame 1306 Coordinates 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bounds (-1) Warning: Frame 2578 Coordinates out of bounds (-1) Warning: Frame 2579 Coordinates out of bounds (-1) Warning: Frame 2580 Coordinates out of bounds (-1) Warning: Frame 2584 Coordinates out of bounds (-1) Warning: Frame 2591 Coordinates out of bounds (-1) Warning: Frame 2592 Coordinates out of bounds (-1) Warning: Frame 2594 Coordinates out of bounds (-1) Warning: Frame 2600 Coordinates out of bounds (-1) Warning: Frame 2601 Coordinates out of bounds (-1) Warning: Frame 2602 Coordinates out of bounds (-1) Warning: Frame 2603 Coordinates out of bounds (-1) Warning: Frame 2604 Coordinates out of bounds (-1) Warning: Frame 2605 Coordinates out of bounds (-1) Warning: Frame 2610 Coordinates out of bounds (-1) Warning: Frame 2623 Coordinates out of bounds (-1) Warning: Frame 2629 Coordinates out of bounds (-1) Warning: Frame 2630 Coordinates out of bounds (-1) Warning: Frame 2639 Coordinates out of bounds (-1) Warning: Frame 2641 Coordinates out of bounds (-1) Warning: Frame 2645 Coordinates out of bounds (-1) Warning: Frame 2648 Coordinates out of bounds (-1) Warning: Frame 2651 Coordinates out of bounds (-1) Warning: Frame 2652 Coordinates out of bounds (-1) Warning: Frame 2653 Coordinates out of bounds (-1) Warning: Frame 2668 Coordinates out of bounds (-1) Warning: Frame 2695 Coordinates out of bounds (-1) Warning: Frame 2716 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 2083 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 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: 2722 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 2722 TIME: Analyses took 0.0015 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 2722 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 2722 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 2722 COM "COM" (double, distance), size is 2722 g1 "g1" (double, torsion(gamma)), size is 2722 d1 "d1" (double, torsion(delta)), size is 2722 e1 "e1" (double, torsion(epsilon)), size is 2722 z1 "z1" (double, torsion(zeta)), size is 2722 c1 "c1" (double, torsion(chin)), size is 2722 a2 "a2" (double, torsion(alpha)), size is 2722 b2 "b2" (double, torsion(beta)), size is 2722 g2 "g2" (double, torsion(gamma)), size is 2722 d2 "d2" (double, torsion(delta)), size is 2722 c2 "c2" (double, torsion(chin)), size is 2722 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 : 0.0000 s ( 0.05%) TIME: Trajectory Process : 0.0071 s ( 13.10%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0015 s ( 2.82%) TIME: Data File Write : 0.0456 s ( 83.99%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0543 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0946 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.