CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 11:07:39 | Available memory: 766.031 MB INPUT: Reading Input from file pt-analysis1.in [parm ../../../build/noWAt.topo.hmr] Reading '../../../build/noWAt.topo.hmr' as Amber Topology [trajin trig.nc] Reading 'trig.nc' 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] Reference mask: [:1,2&!@H*](43) RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [distance dist_sugar_ox :1@O2' :2@O4'] DISTANCE: :1@O2' to :2@O4', center of mass. [distance dist_N3-O5p :1@N3 :1@O5'] DISTANCE: :1@N3 to :1@O5', center of mass. [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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: 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES: 0: 'trig.nc' is a NetCDF AMBER trajectory with replica temperatures, Parm noWAt.topo.hmr (Orthogonal box) (reading 10434 of 10434) Coordinate processing will occur on 10434 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] Target mask: [:1,2&!@H*](43) 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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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) ----- trig.nc (1-10434, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 10434 frames and processed 10434 frames. TIME: Trajectory processing: 0.0811 s TIME: Avg. throughput= 128655.9803 frames / second. ACTION OUTPUT: DATASETS: 16 data sets: noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms rms_2_aform "rms_2_aform" (double, rms), size is 10434 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 10434 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 10434 COM "COM" (double, distance), size is 10434 g1 "g1" (double, torsion(gamma)), size is 10434 d1 "d1" (double, torsion(delta)), size is 10434 e1 "e1" (double, torsion(epsilon)), size is 10434 z1 "z1" (double, torsion(zeta)), size is 10434 c1 "c1" (double, torsion(chin)), size is 10434 a2 "a2" (double, torsion(alpha)), size is 10434 b2 "b2" (double, torsion(beta)), size is 10434 g2 "g2" (double, torsion(gamma)), size is 10434 d2 "d2" (double, torsion(delta)), size is 10434 c2 "c2" (double, torsion(chin)), size is 10434 ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Writing results to avg-rmsd-all.dat [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets: [ COM ] norm: Sum over bins will be normalized to 1.0. [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_N3-O5p ] norm: Sum over bins will be normalized to 1.0. [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets: [ rms_2_aform dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist g1,-180,180,1 out dihed_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 ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 16 analyses: 0: [avg rms_2_aform out avg-rmsd-all.dat] 1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Calculating bins from min=0 max=5 step=0.1. Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 10434 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 269 Coordinates out of bounds (-1) Warning: Frame 1429 Coordinates out of bounds (-1) Warning: Frame 1452 Coordinates out of bounds (-1) Warning: Frame 4566 Coordinates out of bounds (-1) Warning: Frame 6026 Coordinates out of bounds (-1) Warning: Frame 6161 Coordinates out of bounds (-1) Warning: Frame 6163 Coordinates out of bounds (-1) Warning: Frame 6165 Coordinates out of bounds (-1) Warning: Frame 6166 Coordinates out of bounds (-1) Warning: Frame 6385 Coordinates out of bounds (-1) Warning: Frame 8587 Coordinates out of bounds (-1) Warning: Frame 8678 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 10422 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: 10434 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 139 Coordinates out of bounds (-1) Warning: Frame 141 Coordinates out of bounds (-1) Warning: Frame 181 Coordinates out of bounds (-1) Warning: Frame 269 Coordinates out of bounds (-1) Warning: Frame 328 Coordinates out of bounds (-1) Warning: Frame 437 Coordinates out of bounds (-1) Warning: Frame 438 Coordinates out of bounds (-1) Warning: Frame 441 Coordinates out of bounds (-1) Warning: Frame 442 Coordinates out of bounds (-1) Warning: Frame 459 Coordinates out of bounds (-1) Warning: Frame 474 Coordinates out of bounds (-1) Warning: Frame 524 Coordinates out of bounds (-1) Warning: Frame 526 Coordinates out of bounds (-1) Warning: Frame 543 Coordinates out of bounds (-1) Warning: Frame 544 Coordinates out of bounds (-1) Warning: Frame 545 Coordinates out of bounds (-1) Warning: Frame 551 Coordinates out of bounds (-1) Warning: Frame 552 Coordinates out of bounds (-1) Warning: Frame 578 Coordinates out of bounds (-1) Warning: Frame 583 Coordinates out of bounds (-1) Warning: Frame 599 Coordinates out of bounds (-1) Warning: Frame 600 Coordinates out of bounds (-1) Warning: Frame 601 Coordinates out of bounds (-1) Warning: Frame 653 Coordinates out of bounds (-1) Warning: Frame 768 Coordinates out of bounds (-1) Warning: Frame 844 Coordinates out of bounds (-1) Warning: Frame 971 Coordinates out of bounds (-1) Warning: Frame 972 Coordinates out of bounds (-1) Warning: Frame 978 Coordinates out of bounds (-1) Warning: Frame 979 Coordinates out of bounds (-1) Warning: Frame 1153 Coordinates out of bounds (-1) Warning: Frame 1154 Coordinates out of bounds (-1) Warning: Frame 1158 Coordinates out of bounds (-1) Warning: Frame 1160 Coordinates out of bounds (-1) Warning: Frame 1252 Coordinates out of bounds (-1) Warning: Frame 1253 Coordinates out of bounds (-1) Warning: Frame 1326 Coordinates out of bounds (-1) Warning: Frame 1429 Coordinates out of bounds (-1) Warning: Frame 1430 Coordinates out of bounds (-1) Warning: Frame 1431 Coordinates out of bounds (-1) Warning: Frame 1452 Coordinates out of bounds (-1) Warning: Frame 1703 Coordinates out of bounds (-1) Warning: Frame 1756 Coordinates out of bounds (-1) Warning: Frame 1758 Coordinates out of bounds (-1) Warning: Frame 1765 Coordinates out of bounds (-1) Warning: Frame 1860 Coordinates out of bounds (-1) Warning: Frame 1862 Coordinates out of bounds (-1) Warning: Frame 1919 Coordinates out of bounds (-1) Warning: Frame 1921 Coordinates out of bounds (-1) Warning: Frame 1933 Coordinates out of bounds (-1) Warning: Frame 1965 Coordinates out of bounds (-1) Warning: Frame 1978 Coordinates out of bounds (-1) Warning: Frame 2008 Coordinates out of bounds (-1) Warning: Frame 2057 Coordinates out of bounds (-1) Warning: Frame 2058 Coordinates out of bounds (-1) Warning: Frame 2065 Coordinates out of bounds (-1) Warning: Frame 2372 Coordinates out of bounds (-1) Warning: Frame 2374 Coordinates out of bounds (-1) Warning: Frame 2376 Coordinates out of bounds (-1) Warning: Frame 2378 Coordinates out of bounds (-1) Warning: Frame 2446 Coordinates out of bounds (-1) Warning: Frame 2447 Coordinates out of bounds (-1) Warning: Frame 2490 Coordinates out of bounds (-1) Warning: Frame 2654 Coordinates out of bounds (-1) Warning: Frame 2655 Coordinates out of bounds (-1) Warning: Frame 2657 Coordinates out of bounds (-1) Warning: Frame 2658 Coordinates out of bounds (-1) Warning: Frame 2659 Coordinates out of bounds (-1) Warning: Frame 2660 Coordinates out of bounds (-1) Warning: Frame 2809 Coordinates out of bounds (-1) Warning: Frame 2824 Coordinates out of bounds (-1) Warning: Frame 2874 Coordinates out of bounds (-1) Warning: Frame 2875 Coordinates out of bounds (-1) Warning: Frame 2876 Coordinates out of bounds (-1) Warning: Frame 2877 Coordinates out of bounds (-1) Warning: Frame 2884 Coordinates out of bounds (-1) Warning: Frame 2885 Coordinates out of bounds (-1) Warning: Frame 3430 Coordinates out of bounds (-1) Warning: Frame 3522 Coordinates out of bounds (-1) Warning: Frame 3523 Coordinates out of bounds (-1) Warning: Frame 3527 Coordinates out of bounds (-1) Warning: Frame 3529 Coordinates out of bounds (-1) Warning: Frame 3794 Coordinates out of bounds (-1) Warning: Frame 3849 Coordinates out of bounds (-1) Warning: Frame 4046 Coordinates out of bounds (-1) Warning: Frame 4081 Coordinates out of bounds (-1) Warning: Frame 4141 Coordinates out of bounds (-1) Warning: Frame 4142 Coordinates out of bounds (-1) Warning: Frame 4143 Coordinates out of bounds (-1) Warning: Frame 4194 Coordinates out of bounds (-1) Warning: Frame 4196 Coordinates out of bounds (-1) Warning: Frame 4199 Coordinates out of bounds (-1) Warning: Frame 4200 Coordinates out of bounds (-1) Warning: Frame 4385 Coordinates out of bounds (-1) Warning: Frame 4387 Coordinates out of bounds (-1) Warning: Frame 4389 Coordinates out of bounds (-1) Warning: Frame 4414 Coordinates out of bounds (-1) Warning: Frame 4443 Coordinates out of bounds (-1) Warning: Frame 4448 Coordinates out of bounds (-1) Warning: Frame 4453 Coordinates out of bounds (-1) Warning: Frame 4455 Coordinates out of bounds (-1) Warning: Frame 4547 Coordinates out of bounds (-1) Warning: Frame 4549 Coordinates out of bounds (-1) Warning: Frame 4552 Coordinates out of bounds (-1) Warning: Frame 4554 Coordinates out of bounds (-1) Warning: Frame 4555 Coordinates out of bounds (-1) Warning: Frame 4556 Coordinates out of bounds (-1) Warning: Frame 4557 Coordinates out of bounds (-1) Warning: Frame 4561 Coordinates out of bounds (-1) Warning: Frame 4562 Coordinates out of bounds (-1) Warning: Frame 4566 Coordinates out of bounds (-1) Warning: Frame 4568 Coordinates out of bounds (-1) Warning: Frame 4569 Coordinates out of bounds (-1) Warning: Frame 4587 Coordinates out of bounds (-1) Warning: Frame 4702 Coordinates out of bounds (-1) Warning: Frame 4705 Coordinates out of bounds (-1) Warning: Frame 4761 Coordinates out of bounds (-1) Warning: Frame 4889 Coordinates out of bounds (-1) Warning: Frame 4900 Coordinates out of bounds (-1) Warning: Frame 4907 Coordinates out of bounds (-1) Warning: Frame 4908 Coordinates out of bounds (-1) Warning: Frame 4909 Coordinates out of bounds (-1) Warning: Frame 4913 Coordinates out of bounds (-1) Warning: Frame 4920 Coordinates out of bounds (-1) Warning: Frame 4922 Coordinates out of bounds (-1) Warning: Frame 4923 Coordinates out of bounds (-1) Warning: Frame 4924 Coordinates out of bounds (-1) Warning: Frame 4925 Coordinates out of bounds (-1) Warning: Frame 4929 Coordinates out of bounds (-1) Warning: Frame 5012 Coordinates out of bounds (-1) Warning: Frame 5094 Coordinates out of bounds (-1) Warning: Frame 5173 Coordinates out of bounds (-1) Warning: Frame 5179 Coordinates out of bounds (-1) Warning: Frame 5180 Coordinates out of bounds (-1) Warning: Frame 5371 Coordinates out of bounds (-1) Warning: Frame 5372 Coordinates out of bounds (-1) Warning: Frame 5373 Coordinates out of bounds (-1) Warning: Frame 5496 Coordinates out of bounds (-1) Warning: Frame 5651 Coordinates out of bounds (-1) Warning: Frame 5652 Coordinates out of bounds (-1) Warning: Frame 5653 Coordinates out of bounds (-1) Warning: Frame 5670 Coordinates out of bounds (-1) Warning: Frame 6000 Coordinates out of bounds (-1) Warning: Frame 6001 Coordinates out of bounds (-1) Warning: Frame 6026 Coordinates out of bounds (-1) Warning: Frame 6096 Coordinates out of bounds (-1) Warning: Frame 6161 Coordinates out of bounds (-1) Warning: Frame 6162 Coordinates out of bounds (-1) Warning: Frame 6163 Coordinates out of bounds (-1) Warning: Frame 6164 Coordinates out of bounds (-1) Warning: Frame 6165 Coordinates out of bounds (-1) Warning: Frame 6166 Coordinates out of bounds (-1) Warning: Frame 6169 Coordinates out of bounds (-1) Warning: Frame 6172 Coordinates out of bounds (-1) Warning: Frame 6173 Coordinates out of bounds (-1) Warning: Frame 6376 Coordinates out of bounds (-1) Warning: Frame 6380 Coordinates out of bounds (-1) Warning: Frame 6384 Coordinates out of bounds (-1) Warning: Frame 6385 Coordinates out of bounds (-1) Warning: Frame 6585 Coordinates out of bounds (-1) Warning: Frame 6620 Coordinates out of bounds (-1) Warning: Frame 6630 Coordinates out of bounds (-1) Warning: Frame 6631 Coordinates out of bounds (-1) Warning: Frame 6632 Coordinates out of bounds (-1) Warning: Frame 6633 Coordinates out of bounds (-1) Warning: Frame 6634 Coordinates out of bounds (-1) Warning: Frame 6636 Coordinates out of bounds (-1) Warning: Frame 6637 Coordinates out of bounds (-1) Warning: Frame 6638 Coordinates out of bounds (-1) Warning: Frame 6639 Coordinates out of bounds (-1) Warning: Frame 6786 Coordinates out of bounds (-1) Warning: Frame 6818 Coordinates out of bounds (-1) Warning: Frame 6819 Coordinates out of bounds (-1) Warning: Frame 6820 Coordinates out of bounds (-1) Warning: Frame 6972 Coordinates out of bounds (-1) Warning: Frame 6973 Coordinates out of bounds (-1) Warning: Frame 7007 Coordinates out of bounds (-1) Warning: Frame 7008 Coordinates out of bounds (-1) Warning: Frame 7009 Coordinates out of bounds (-1) Warning: Frame 7049 Coordinates out of bounds (-1) Warning: Frame 7072 Coordinates out of bounds (-1) Warning: Frame 7073 Coordinates out of bounds (-1) Warning: Frame 7183 Coordinates out of bounds (-1) Warning: Frame 7221 Coordinates out of bounds (-1) Warning: Frame 7222 Coordinates out of bounds (-1) Warning: Frame 7236 Coordinates out of bounds (-1) Warning: Frame 7245 Coordinates out of bounds (-1) Warning: Frame 7247 Coordinates out of bounds (-1) Warning: Frame 7305 Coordinates out of bounds (-1) Warning: Frame 7438 Coordinates out of bounds (-1) Warning: Frame 7440 Coordinates out of bounds (-1) Warning: Frame 7463 Coordinates out of bounds (-1) Warning: Frame 7464 Coordinates out of bounds (-1) Warning: Frame 7519 Coordinates out of bounds (-1) Warning: Frame 7541 Coordinates out of bounds (-1) Warning: Frame 7565 Coordinates out of bounds (-1) Warning: Frame 7601 Coordinates out of bounds (-1) Warning: Frame 7602 Coordinates out of bounds (-1) Warning: Frame 7654 Coordinates out of bounds (-1) Warning: Frame 7798 Coordinates out of bounds (-1) Warning: Frame 7967 Coordinates out of bounds (-1) Warning: Frame 7975 Coordinates out of bounds (-1) Warning: Frame 7995 Coordinates out of bounds (-1) Warning: Frame 8002 Coordinates out of bounds (-1) Warning: Frame 8092 Coordinates out of bounds (-1) Warning: Frame 8093 Coordinates out of bounds (-1) Warning: Frame 8094 Coordinates out of bounds (-1) Warning: Frame 8095 Coordinates out of bounds (-1) Warning: Frame 8114 Coordinates out of bounds (-1) Warning: Frame 8505 Coordinates out of bounds (-1) Warning: Frame 8547 Coordinates out of bounds (-1) Warning: Frame 8587 Coordinates out of bounds (-1) Warning: Frame 8595 Coordinates out of bounds (-1) Warning: Frame 8605 Coordinates out of bounds (-1) Warning: Frame 8678 Coordinates out of bounds (-1) Warning: Frame 8679 Coordinates out of bounds (-1) Warning: Frame 8700 Coordinates out of bounds (-1) Warning: Frame 8701 Coordinates out of bounds (-1) Warning: Frame 8702 Coordinates out of bounds (-1) Warning: Frame 8703 Coordinates out of bounds (-1) Warning: Frame 8749 Coordinates out of bounds (-1) Warning: Frame 8755 Coordinates out of bounds (-1) Warning: Frame 8759 Coordinates out of bounds (-1) Warning: Frame 8774 Coordinates out of bounds (-1) Warning: Frame 8775 Coordinates out of bounds (-1) Warning: Frame 8776 Coordinates out of bounds (-1) Warning: Frame 8778 Coordinates out of bounds (-1) Warning: Frame 8779 Coordinates out of bounds (-1) Warning: Frame 8866 Coordinates out of bounds (-1) Warning: Frame 8944 Coordinates out of bounds (-1) Warning: Frame 8972 Coordinates out of bounds (-1) Warning: Frame 9308 Coordinates out of bounds (-1) Warning: Frame 9529 Coordinates out of bounds (-1) Warning: Frame 9537 Coordinates out of bounds (-1) Warning: Frame 9559 Coordinates out of bounds (-1) Warning: Frame 9568 Coordinates out of bounds (-1) Warning: Frame 9590 Coordinates out of bounds (-1) Warning: Frame 9591 Coordinates out of bounds (-1) Warning: Frame 9794 Coordinates out of bounds (-1) Warning: Frame 9817 Coordinates out of bounds (-1) Warning: Frame 9818 Coordinates out of bounds (-1) Warning: Frame 9914 Coordinates out of bounds (-1) Warning: Frame 9915 Coordinates out of bounds (-1) Warning: Frame 9919 Coordinates out of bounds (-1) Warning: Frame 9920 Coordinates out of bounds (-1) Warning: Frame 9921 Coordinates out of bounds (-1) Warning: Frame 9922 Coordinates out of bounds (-1) Warning: Frame 9923 Coordinates out of bounds (-1) Warning: Frame 9992 Coordinates out of bounds (-1) Warning: Frame 10035 Coordinates out of bounds (-1) Warning: Frame 10036 Coordinates out of bounds (-1) Warning: Frame 10049 Coordinates out of bounds (-1) Warning: Frame 10069 Coordinates out of bounds (-1) Warning: Frame 10162 Coordinates out of bounds (-1) Warning: Frame 10183 Coordinates out of bounds (-1) Warning: Frame 10215 Coordinates out of bounds (-1) Warning: Frame 10216 Coordinates out of bounds (-1) Warning: Frame 10401 Coordinates out of bounds (-1) Warning: Frame 10409 Coordinates out of bounds (-1) Warning: Frame 10410 Coordinates out of bounds (-1) Warning: Frame 10421 Coordinates out of bounds (-1) Warning: Frame 10424 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 10172 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: 10434 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 10434 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: 10434 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 10434 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: 10434 data points in each dimension. Hist: Allocating histogram, total bins = 5000 Warning: Frame 269 Coordinates out of bounds (-1) Warning: Frame 1429 Coordinates out of bounds (-1) Warning: Frame 1452 Coordinates out of bounds (-1) Warning: Frame 4566 Coordinates out of bounds (-1) Warning: Frame 6026 Coordinates out of bounds (-1) Warning: Frame 6161 Coordinates out of bounds (-1) Warning: Frame 6163 Coordinates out of bounds (-1) Warning: Frame 6165 Coordinates out of bounds (-1) Warning: Frame 6166 Coordinates out of bounds (-1) Warning: Frame 6385 Coordinates out of bounds (-1) Warning: Frame 8587 Coordinates out of bounds (-1) Warning: Frame 8678 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 10422 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 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: 10434 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 10434 TIME: Analyses took 0.0022 seconds. DATASETS: 31 data sets: noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms rms_2_aform "rms_2_aform" (double, rms), size is 10434 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 10434 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 10434 COM "COM" (double, distance), size is 10434 g1 "g1" (double, torsion(gamma)), size is 10434 d1 "d1" (double, torsion(delta)), size is 10434 e1 "e1" (double, torsion(epsilon)), size is 10434 z1 "z1" (double, torsion(zeta)), size is 10434 c1 "c1" (double, torsion(chin)), size is 10434 a2 "a2" (double, torsion(alpha)), size is 10434 b2 "b2" (double, torsion(beta)), size is 10434 g2 "g2" (double, torsion(gamma)), size is 10434 d2 "d2" (double, torsion(delta)), size is 10434 c2 "c2" (double, torsion(chin)), size is 10434 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 Hist_00018 "Hist_00018" (double), size is 100 Hist_00019 "Hist_00019" (double), size is 100 Hist_00020 "Hist_00020" (double matrix), size is 5000 gamma_1 "gamma_1" (double), size is 360 delta_1 "delta_1" (double), size is 360 epsilon_1 "epsilon_1" (double), size is 360 zeta_1 "zeta_1" (double), size is 360 chi_1 "chi_1" (double), size is 360 alpha_2 "alpha_2" (double), size is 360 beta_2 "beta_2" (double), size is 360 gamma_2 "gamma_2" (double), size is 360 delta_2 "delta_2" (double), size is 360 chi_2 "chi_2" (double), size is 360 DATAFILES: rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM distO2O4-hist.dat (Standard Data File): Hist_00018 distN3-O5p-hist.dat (Standard Data File): Hist_00019 2dhist_rms-dist.gnu (Gnuplot File): Hist_00020 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 avg-rmsd-all.dat (DataSet Average) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.3451 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.