CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 10:59:34 | Available memory: 5591.81 MB INPUT: Reading Input from file pt-analysis1.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c1] Reading '../ctraj.c1' as Amber NetCDF [reference ../../../A-form.pdb [a-form]] Reading '../../../A-form.pdb' as PDB [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [distance dist_sugar_ox :1@O2' :2@O4' ] DISTANCE: :1@O2' to :2@O4', center of mass. [distance dist_N3-O5p :1@N3 :1@O5'] DISTANCE: :1@N3 to :1@O5', center of mass. [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 165204 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 165204 of 165204) Coordinate processing will occur on 165204 frames. REFERENCE FRAMES (1 total): 0: '../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0009 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Target mask: [:1,2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 1: [distance dist_sugar_ox :1@O2' :2@O4' ] :1@O2' (1 atoms) to :2@O4' (1 atoms), imaged. 2: [distance dist_N3-O5p :1@N3 :1@O5'] :1@N3 (1 atoms) to :1@O5' (1 atoms), imaged. 3: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 8: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- ctraj.c1 (1-165204, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 165204 frames and processed 165204 frames. TIME: Trajectory processing: 0.6330 s TIME: Avg. throughput= 260996.0899 frames / second. ACTION OUTPUT: DATASETS: 15 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 165204 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 165204 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 165204 COM "COM" (double, distance), size is 165204 g1 "g1" (double, torsion(gamma)), size is 165204 d1 "d1" (double, torsion(delta)), size is 165204 e1 "e1" (double, torsion(epsilon)), size is 165204 z1 "z1" (double, torsion(zeta)), size is 165204 c1 "c1" (double, torsion(chi)), size is 165204 a2 "a2" (double, torsion(alpha)), size is 165204 b2 "b2" (double, torsion(beta)), size is 165204 g2 "g2" (double, torsion(gamma)), size is 165204 d2 "d2" (double, torsion(delta)), size is 165204 c2 "c2" (double, torsion(chi)), size is 165204 ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Writing results to avg-rmsd-all.dat [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets: [ COM ] norm: Sum over bins will be normalized to 1.0. [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_N3-O5p ] norm: Sum over bins will be normalized to 1.0. [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets: [ rms_2_aform dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm] Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets: [ g1 ] norm: Sum over bins will be normalized to 1.0. [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets: [ d1 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets: [ e1 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets: [ z1 ] norm: Sum over bins will be normalized to 1.0. [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets: [ c1 ] norm: Sum over bins will be normalized to 1.0. [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets: [ a2 ] norm: Sum over bins will be normalized to 1.0. [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets: [ b2 ] norm: Sum over bins will be normalized to 1.0. [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets: [ g2 ] norm: Sum over bins will be normalized to 1.0. [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets: [ d2 ] norm: Sum over bins will be normalized to 1.0. [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets: [ c2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 16 analyses: 0: [avg rms_2_aform out avg-rmsd-all.dat] 1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 165204 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 165204.000000 2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Dim COM: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 165204 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 2958 Coordinates out of bounds (-1) Warning: Frame 3242 Coordinates out of bounds (-1) Warning: Frame 3412 Coordinates out of bounds (-1) Warning: Frame 3434 Coordinates out of bounds (-1) Warning: Frame 4628 Coordinates out of bounds (-1) Warning: Frame 5955 Coordinates out of bounds (-1) Warning: Frame 7908 Coordinates out of bounds (-1) Warning: Frame 15819 Coordinates out of bounds (-1) Warning: Frame 22534 Coordinates out of bounds (-1) Warning: Frame 28112 Coordinates out of bounds (-1) Warning: Frame 30178 Coordinates out of bounds (-1) Warning: Frame 30181 Coordinates out of bounds (-1) Warning: Frame 36149 Coordinates out of bounds (-1) Warning: Frame 36281 Coordinates out of bounds (-1) Warning: Frame 37689 Coordinates out of bounds (-1) Warning: Frame 37784 Coordinates out of bounds (-1) Warning: Frame 37789 Coordinates out of bounds (-1) Warning: Frame 37790 Coordinates out of bounds (-1) Warning: Frame 45191 Coordinates out of bounds (-1) Warning: Frame 46792 Coordinates out of bounds (-1) Warning: Frame 46793 Coordinates out of bounds (-1) Warning: Frame 47108 Coordinates out of bounds (-1) Warning: Frame 48517 Coordinates out of bounds (-1) Warning: Frame 48587 Coordinates out of bounds (-1) Warning: Frame 48852 Coordinates out of bounds (-1) Warning: Frame 51181 Coordinates out of bounds (-1) Warning: Frame 57438 Coordinates out of bounds (-1) Warning: Frame 57728 Coordinates out of bounds (-1) Warning: Frame 58280 Coordinates out of bounds (-1) Warning: Frame 58471 Coordinates out of bounds (-1) Warning: Frame 58473 Coordinates out of bounds (-1) Warning: Frame 59182 Coordinates out of bounds (-1) Warning: Frame 59194 Coordinates out of bounds (-1) Warning: Frame 68117 Coordinates out of bounds (-1) Warning: Frame 70958 Coordinates out of bounds (-1) Warning: Frame 72594 Coordinates out of bounds (-1) Warning: Frame 80099 Coordinates out of bounds (-1) Warning: Frame 80934 Coordinates out of bounds (-1) Warning: Frame 81917 Coordinates out of bounds (-1) Warning: Frame 81918 Coordinates out of bounds (-1) Warning: Frame 82077 Coordinates out of bounds (-1) Warning: Frame 82645 Coordinates out of bounds (-1) Warning: Frame 82833 Coordinates out of bounds (-1) Warning: Frame 82944 Coordinates out of bounds (-1) Warning: Frame 84786 Coordinates out of bounds (-1) Warning: Frame 84878 Coordinates out of bounds (-1) Warning: Frame 85464 Coordinates out of bounds (-1) Warning: Frame 88095 Coordinates out of bounds (-1) Warning: Frame 88761 Coordinates out of bounds (-1) Warning: Frame 88762 Coordinates out of bounds (-1) Warning: Frame 90175 Coordinates out of bounds (-1) Warning: Frame 90743 Coordinates out of bounds (-1) Warning: Frame 90976 Coordinates out of bounds (-1) Warning: Frame 91099 Coordinates out of bounds (-1) Warning: Frame 91224 Coordinates out of bounds (-1) Warning: Frame 91489 Coordinates out of bounds (-1) Warning: Frame 91928 Coordinates out of bounds (-1) Warning: Frame 91961 Coordinates out of bounds (-1) Warning: Frame 92013 Coordinates out of bounds (-1) Warning: Frame 92074 Coordinates out of bounds (-1) Warning: Frame 92122 Coordinates out of bounds (-1) Warning: Frame 92248 Coordinates out of bounds (-1) Warning: Frame 92391 Coordinates out of bounds (-1) Warning: Frame 92396 Coordinates out of bounds (-1) Warning: Frame 93019 Coordinates out of bounds (-1) Warning: Frame 93512 Coordinates out of bounds (-1) Warning: Frame 93567 Coordinates out of bounds (-1) Warning: Frame 93568 Coordinates out of bounds (-1) Warning: Frame 94298 Coordinates out of bounds (-1) Warning: Frame 94886 Coordinates out of bounds (-1) Warning: Frame 94953 Coordinates out of bounds (-1) Warning: Frame 95202 Coordinates out of bounds (-1) Warning: Frame 95414 Coordinates out of bounds (-1) Warning: Frame 96641 Coordinates out of bounds (-1) Warning: Frame 96734 Coordinates out of bounds (-1) Warning: Frame 97128 Coordinates out of bounds (-1) Warning: Frame 97152 Coordinates out of bounds (-1) Warning: Frame 97336 Coordinates out of bounds (-1) Warning: Frame 97669 Coordinates out of bounds (-1) Warning: Frame 98281 Coordinates out of bounds (-1) Warning: Frame 98797 Coordinates out of bounds (-1) Warning: Frame 98830 Coordinates out of bounds (-1) Warning: Frame 98831 Coordinates out of bounds (-1) Warning: Frame 98874 Coordinates out of bounds (-1) Warning: Frame 98899 Coordinates out of bounds (-1) Warning: Frame 99306 Coordinates out of bounds (-1) Warning: Frame 99618 Coordinates out of bounds (-1) Warning: Frame 99848 Coordinates out of bounds (-1) Warning: Frame 100131 Coordinates out of bounds (-1) Warning: Frame 100137 Coordinates out of bounds (-1) Warning: Frame 100716 Coordinates out of bounds (-1) Warning: Frame 100869 Coordinates out of bounds (-1) Warning: Frame 100903 Coordinates out of bounds (-1) Warning: Frame 100984 Coordinates out of bounds (-1) Warning: Frame 101022 Coordinates out of bounds (-1) Warning: Frame 101027 Coordinates out of bounds (-1) Warning: Frame 101028 Coordinates out of bounds (-1) Warning: Frame 101225 Coordinates out of bounds (-1) Warning: Frame 101541 Coordinates out of bounds (-1) Warning: Frame 101609 Coordinates out of bounds (-1) Warning: Frame 101745 Coordinates out of bounds (-1) Warning: Frame 102204 Coordinates out of bounds (-1) Warning: Frame 102337 Coordinates out of bounds (-1) Warning: Frame 102595 Coordinates out of bounds (-1) Warning: Frame 102636 Coordinates out of bounds (-1) Warning: Frame 102639 Coordinates out of bounds (-1) Warning: Frame 102785 Coordinates out of bounds (-1) Warning: Frame 103220 Coordinates out of bounds (-1) Warning: Frame 103455 Coordinates out of bounds (-1) Warning: Frame 104036 Coordinates out of bounds (-1) Warning: Frame 104188 Coordinates out of bounds (-1) Warning: Frame 104548 Coordinates out of bounds (-1) Warning: Frame 104890 Coordinates out of bounds (-1) Warning: Frame 104908 Coordinates out of bounds (-1) Warning: Frame 105025 Coordinates out of bounds (-1) Warning: Frame 105322 Coordinates out of bounds (-1) Warning: Frame 105362 Coordinates out of bounds (-1) Warning: Frame 105392 Coordinates out of bounds (-1) Warning: Frame 105447 Coordinates out of bounds (-1) Warning: Frame 105543 Coordinates out of bounds (-1) Warning: Frame 105948 Coordinates out of bounds (-1) Warning: Frame 106153 Coordinates out of bounds (-1) Warning: Frame 106189 Coordinates out of bounds (-1) Warning: Frame 106237 Coordinates out of bounds (-1) Warning: Frame 106274 Coordinates out of bounds (-1) Warning: Frame 106535 Coordinates out of bounds (-1) Warning: Frame 106538 Coordinates out of bounds (-1) Warning: Frame 106674 Coordinates out of bounds (-1) Warning: Frame 106717 Coordinates out of bounds (-1) Warning: Frame 107057 Coordinates out of bounds (-1) Warning: Frame 107072 Coordinates out of bounds (-1) Warning: Frame 107299 Coordinates out of bounds (-1) Warning: Frame 107913 Coordinates out of bounds (-1) Warning: Frame 107950 Coordinates out of bounds (-1) Warning: Frame 108020 Coordinates out of bounds (-1) Warning: Frame 108304 Coordinates out of bounds (-1) Warning: Frame 108729 Coordinates out of bounds (-1) Warning: Frame 108841 Coordinates out of bounds (-1) Warning: Frame 109099 Coordinates out of bounds (-1) Warning: Frame 109300 Coordinates out of bounds (-1) Warning: Frame 110112 Coordinates out of bounds (-1) Warning: Frame 110597 Coordinates out of bounds (-1) Warning: Frame 110665 Coordinates out of bounds (-1) Warning: Frame 110686 Coordinates out of bounds (-1) Warning: Frame 111259 Coordinates out of bounds (-1) Warning: Frame 111303 Coordinates out of bounds (-1) Warning: Frame 111703 Coordinates out of bounds (-1) Warning: Frame 111823 Coordinates out of bounds (-1) Warning: Frame 112124 Coordinates out of bounds (-1) Warning: Frame 112125 Coordinates out of bounds (-1) Warning: Frame 112509 Coordinates out of bounds (-1) Warning: Frame 112884 Coordinates out of bounds (-1) Warning: Frame 113635 Coordinates out of bounds (-1) Warning: Frame 113762 Coordinates out of bounds (-1) Warning: Frame 113982 Coordinates out of bounds (-1) Warning: Frame 114082 Coordinates out of bounds (-1) Warning: Frame 114279 Coordinates out of bounds (-1) Warning: Frame 114330 Coordinates out of bounds (-1) Warning: Frame 114346 Coordinates out of bounds (-1) Warning: Frame 114666 Coordinates out of bounds (-1) Warning: Frame 114922 Coordinates out of bounds (-1) Warning: Frame 115718 Coordinates out of bounds (-1) Warning: Frame 116477 Coordinates out of bounds (-1) Warning: Frame 118833 Coordinates out of bounds (-1) Warning: Frame 123300 Coordinates out of bounds (-1) Warning: Frame 123836 Coordinates out of bounds (-1) Warning: Frame 124172 Coordinates out of bounds (-1) Warning: Frame 128319 Coordinates out of bounds (-1) Warning: Frame 128324 Coordinates out of bounds (-1) Warning: Frame 132195 Coordinates out of bounds (-1) Warning: Frame 132656 Coordinates out of bounds (-1) Warning: Frame 133362 Coordinates out of bounds (-1) Warning: Frame 133363 Coordinates out of bounds (-1) Warning: Frame 134726 Coordinates out of bounds (-1) Warning: Frame 134733 Coordinates out of bounds (-1) Warning: Frame 134734 Coordinates out of bounds (-1) Warning: Frame 134735 Coordinates out of bounds (-1) Warning: Frame 138188 Coordinates out of bounds (-1) Warning: Frame 138622 Coordinates out of bounds (-1) Warning: Frame 142474 Coordinates out of bounds (-1) Warning: Frame 144040 Coordinates out of bounds (-1) Warning: Frame 145544 Coordinates out of bounds (-1) Warning: Frame 146804 Coordinates out of bounds (-1) Warning: Frame 146805 Coordinates out of bounds (-1) Warning: Frame 147157 Coordinates out of bounds (-1) Warning: Frame 149083 Coordinates out of bounds (-1) Warning: Frame 149381 Coordinates out of bounds (-1) Warning: Frame 149986 Coordinates out of bounds (-1) Warning: Frame 150523 Coordinates out of bounds (-1) Warning: Frame 151491 Coordinates out of bounds (-1) Warning: Frame 154220 Coordinates out of bounds (-1) Warning: Frame 154231 Coordinates out of bounds (-1) Warning: Frame 154233 Coordinates out of bounds (-1) Warning: Frame 154234 Coordinates out of bounds (-1) Warning: Frame 156431 Coordinates out of bounds (-1) Warning: Frame 158123 Coordinates out of bounds (-1) Warning: Frame 160455 Coordinates out of bounds (-1) Warning: Frame 161840 Coordinates out of bounds (-1) Warning: Frame 161841 Coordinates out of bounds (-1) Warning: Frame 161844 Coordinates out of bounds (-1) Warning: Frame 162321 Coordinates out of bounds (-1) Warning: Frame 164180 Coordinates out of bounds (-1) Warning: Frame 164189 Coordinates out of bounds (-1) Warning: Frame 164190 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 165000.000000 3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 165204 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 165204.000000 4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 165204 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 165204.000000 5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 165204 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 165204.000000 6: [hist g1,-180,180,1 out dihed_a2-hist.dat name gamma_1 norm] Dim g1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Dim d1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Dim e1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Dim b2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Dim g2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Dim d2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Dim c2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 165204 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 165204.000000 TIME: Analyses took 0.0233 seconds. DATASETS: 30 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 165204 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 165204 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 165204 COM "COM" (double, distance), size is 165204 g1 "g1" (double, torsion(gamma)), size is 165204 d1 "d1" (double, torsion(delta)), size is 165204 e1 "e1" (double, torsion(epsilon)), size is 165204 z1 "z1" (double, torsion(zeta)), size is 165204 c1 "c1" (double, torsion(chi)), size is 165204 a2 "a2" (double, torsion(alpha)), size is 165204 b2 "b2" (double, torsion(beta)), size is 165204 g2 "g2" (double, torsion(gamma)), size is 165204 d2 "d2" (double, torsion(delta)), size is 165204 c2 "c2" (double, torsion(chi)), size is 165204 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 Hist_00017 "Hist_00017" (double), size is 100 Hist_00018 "Hist_00018" (double), size is 100 Hist_00019 "Hist_00019" (double matrix), size is 5000 gamma_1 "gamma_1" (double), size is 360 delta_1 "delta_1" (double), size is 360 epsilon_1 "epsilon_1" (double), size is 360 zeta_1 "zeta_1" (double), size is 360 chi_1 "chi_1" (double), size is 360 alpha_2 "alpha_2" (double), size is 360 beta_2 "beta_2" (double), size is 360 gamma_2 "gamma_2" (double), size is 360 delta_2 "delta_2" (double), size is 360 chi_2 "chi_2" (double), size is 360 DATAFILES: rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM distO2O4-hist.dat (Standard Data File): Hist_00017 distN3-O5p-hist.dat (Standard Data File): Hist_00018 2dhist_rms-dist.gnu (Gnuplot File): Hist_00019 dihed_a2-hist.dat (Standard Data File): gamma_1 alpha_2 dihed_d1-hist.dat (Standard Data File): delta_1 dihed_e1-hist.dat (Standard Data File): epsilon_1 dihed_z1-hist.dat (Standard Data File): zeta_1 dihed_c1-hist.dat (Standard Data File): chi_1 dihed_b2-hist.dat (Standard Data File): beta_2 dihed_g2-hist.dat (Standard Data File): gamma_2 dihed_d2-hist.dat (Standard Data File): delta_2 dihed_c2-hist.dat (Standard Data File): chi_2 avg-rmsd-all.dat (DataSet Average) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.9201 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.