CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 20:40:09 | Available memory: 53810.2 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, 226 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 226 of 226) Coordinate processing will occur on 226 frames. REFERENCE FRAMES (1 total): 0: '../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0000 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*](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 (1-226, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 226 frames and processed 226 frames. TIME: Trajectory processing: 0.0037 s TIME: Avg. throughput= 61329.7151 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 226 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 226 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 226 COM "COM" (double, distance), size is 226 g1 "g1" (double, torsion(gamma)), size is 226 d1 "d1" (double, torsion(delta)), size is 226 e1 "e1" (double, torsion(epsilon)), size is 226 z1 "z1" (double, torsion(zeta)), size is 226 c1 "c1" (double, torsion(chi)), size is 226 a2 "a2" (double, torsion(alpha)), size is 226 b2 "b2" (double, torsion(beta)), size is 226 g2 "g2" (double, torsion(gamma)), size is 226 d2 "d2" (double, torsion(delta)), size is 226 c2 "c2" (double, torsion(chi)), size is 226 ---------- 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: 226 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 226.000000 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: 226 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 1 Coordinates out of bounds (-1) Warning: Frame 2 Coordinates out of bounds (-1) Warning: Frame 3 Coordinates out of bounds (-1) Warning: Frame 4 Coordinates out of bounds (-1) Warning: Frame 5 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 11 Coordinates out of bounds (-1) Warning: Frame 12 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 16 Coordinates out of bounds (-1) Warning: Frame 17 Coordinates out of bounds (-1) Warning: Frame 18 Coordinates out of bounds (-1) Warning: Frame 19 Coordinates out of bounds (-1) Warning: Frame 20 Coordinates out of bounds (-1) Warning: Frame 21 Coordinates out of bounds (-1) Warning: Frame 22 Coordinates out of bounds (-1) Warning: Frame 23 Coordinates out of bounds (-1) Warning: Frame 24 Coordinates out of bounds (-1) Warning: Frame 25 Coordinates out of bounds (-1) Warning: Frame 26 Coordinates out of bounds (-1) Warning: Frame 27 Coordinates out of bounds (-1) Warning: Frame 28 Coordinates out of bounds (-1) Warning: Frame 29 Coordinates out of bounds (-1) Warning: Frame 30 Coordinates out of bounds (-1) Warning: Frame 31 Coordinates out of bounds (-1) Warning: Frame 32 Coordinates out of bounds (-1) Warning: Frame 33 Coordinates out of bounds (-1) Warning: Frame 34 Coordinates out of bounds (-1) Warning: Frame 35 Coordinates out of bounds (-1) Warning: Frame 36 Coordinates out of bounds (-1) Warning: Frame 37 Coordinates out of bounds (-1) Warning: Frame 38 Coordinates out of bounds (-1) Warning: Frame 39 Coordinates out of bounds (-1) Warning: Frame 40 Coordinates out of bounds (-1) Warning: Frame 41 Coordinates out of bounds (-1) Warning: Frame 42 Coordinates out of bounds (-1) Warning: Frame 43 Coordinates out of bounds (-1) Warning: Frame 44 Coordinates out of bounds (-1) Warning: Frame 45 Coordinates out of bounds (-1) Warning: Frame 46 Coordinates out of bounds (-1) Warning: Frame 47 Coordinates out of bounds (-1) Warning: Frame 48 Coordinates out of bounds (-1) Warning: Frame 49 Coordinates out of bounds (-1) Warning: Frame 50 Coordinates out of bounds (-1) Warning: Frame 51 Coordinates out of bounds (-1) Warning: Frame 52 Coordinates out of bounds (-1) Warning: Frame 53 Coordinates out of bounds (-1) Warning: Frame 54 Coordinates out of bounds (-1) Warning: Frame 55 Coordinates out of bounds (-1) Warning: Frame 56 Coordinates out of bounds (-1) Warning: Frame 57 Coordinates out of bounds (-1) Warning: Frame 58 Coordinates out of bounds (-1) Warning: Frame 59 Coordinates out of bounds (-1) Warning: Frame 60 Coordinates out of bounds (-1) Warning: Frame 61 Coordinates out of bounds (-1) Warning: Frame 62 Coordinates out of bounds (-1) Warning: Frame 63 Coordinates out of bounds (-1) Warning: Frame 64 Coordinates out of bounds (-1) Warning: Frame 65 Coordinates out of bounds (-1) Warning: Frame 66 Coordinates out of bounds (-1) Warning: Frame 67 Coordinates out of bounds (-1) Warning: Frame 68 Coordinates out of bounds (-1) Warning: Frame 69 Coordinates out of bounds (-1) Warning: Frame 70 Coordinates out of bounds (-1) Warning: Frame 71 Coordinates out of bounds (-1) Warning: Frame 72 Coordinates out of bounds (-1) Warning: Frame 73 Coordinates out of bounds (-1) Warning: Frame 74 Coordinates out of bounds (-1) Warning: Frame 75 Coordinates out of bounds (-1) Warning: Frame 76 Coordinates out of bounds (-1) Warning: Frame 77 Coordinates out of bounds (-1) Warning: Frame 78 Coordinates out of bounds (-1) Warning: Frame 79 Coordinates out of bounds (-1) Warning: Frame 80 Coordinates out of bounds (-1) Warning: Frame 81 Coordinates out of bounds (-1) Warning: Frame 82 Coordinates out of bounds (-1) Warning: Frame 83 Coordinates out of bounds (-1) Warning: Frame 84 Coordinates out of bounds (-1) Warning: Frame 85 Coordinates out of bounds (-1) Warning: Frame 86 Coordinates out of bounds (-1) Warning: Frame 87 Coordinates out of bounds (-1) Warning: Frame 88 Coordinates out of bounds (-1) Warning: Frame 89 Coordinates out of bounds (-1) Warning: Frame 90 Coordinates out of bounds (-1) Warning: Frame 91 Coordinates out of bounds (-1) Warning: Frame 92 Coordinates out of bounds (-1) Warning: Frame 93 Coordinates out of bounds (-1) Warning: Frame 94 Coordinates out of bounds (-1) Warning: Frame 95 Coordinates out of bounds (-1) Warning: Frame 96 Coordinates out of bounds (-1) Warning: Frame 97 Coordinates out of bounds (-1) Warning: Frame 98 Coordinates out of bounds (-1) Warning: Frame 99 Coordinates out of bounds (-1) Warning: Frame 100 Coordinates out of bounds (-1) Warning: Frame 101 Coordinates out of bounds (-1) Warning: Frame 102 Coordinates out of bounds (-1) Warning: Frame 103 Coordinates out of bounds (-1) Warning: Frame 104 Coordinates out of bounds (-1) Warning: Frame 105 Coordinates out of bounds (-1) Warning: Frame 106 Coordinates out of bounds (-1) Warning: Frame 107 Coordinates out of bounds (-1) Warning: Frame 108 Coordinates out of bounds (-1) Warning: Frame 109 Coordinates out of bounds (-1) Warning: Frame 110 Coordinates out of bounds (-1) Warning: Frame 111 Coordinates out of bounds (-1) Warning: Frame 112 Coordinates out of bounds (-1) Warning: Frame 113 Coordinates out of bounds (-1) Warning: Frame 114 Coordinates out of bounds (-1) Warning: Frame 115 Coordinates out of bounds (-1) Warning: Frame 116 Coordinates out of bounds (-1) Warning: Frame 117 Coordinates out of bounds (-1) Warning: Frame 118 Coordinates out of bounds (-1) Warning: Frame 119 Coordinates out of bounds (-1) Warning: Frame 120 Coordinates out of bounds (-1) Warning: Frame 121 Coordinates out of bounds (-1) Warning: Frame 122 Coordinates out of bounds (-1) Warning: Frame 123 Coordinates out of bounds (-1) Warning: Frame 124 Coordinates out of bounds (-1) Warning: Frame 125 Coordinates out of bounds (-1) Warning: Frame 126 Coordinates out of bounds (-1) Warning: Frame 127 Coordinates out of bounds (-1) Warning: Frame 128 Coordinates out of bounds (-1) Warning: Frame 129 Coordinates out of bounds (-1) Warning: Frame 130 Coordinates out of bounds (-1) Warning: Frame 131 Coordinates out of bounds (-1) Warning: Frame 132 Coordinates out of bounds (-1) Warning: Frame 133 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 138 Coordinates out of bounds (-1) Warning: Frame 139 Coordinates out of bounds (-1) Warning: Frame 140 Coordinates out of bounds (-1) Warning: Frame 141 Coordinates out of bounds (-1) Warning: Frame 142 Coordinates out of bounds (-1) Warning: Frame 143 Coordinates out of bounds (-1) Warning: Frame 144 Coordinates out of bounds (-1) Warning: Frame 145 Coordinates out of bounds (-1) Warning: Frame 146 Coordinates out of bounds (-1) Warning: Frame 147 Coordinates out of bounds (-1) Warning: Frame 148 Coordinates out of bounds (-1) Warning: Frame 149 Coordinates out of bounds (-1) Warning: Frame 150 Coordinates out of bounds (-1) Warning: Frame 151 Coordinates out of bounds (-1) Warning: Frame 152 Coordinates out of bounds (-1) Warning: Frame 153 Coordinates out of bounds (-1) Warning: Frame 154 Coordinates out of bounds (-1) Warning: Frame 155 Coordinates out of bounds (-1) Warning: Frame 156 Coordinates out of bounds (-1) Warning: Frame 157 Coordinates out of bounds (-1) Warning: Frame 158 Coordinates out of bounds (-1) Warning: Frame 159 Coordinates out of bounds (-1) Warning: Frame 160 Coordinates out of bounds (-1) Warning: Frame 161 Coordinates out of bounds (-1) Warning: Frame 162 Coordinates out of bounds (-1) Warning: Frame 163 Coordinates out of bounds (-1) Warning: Frame 164 Coordinates out of bounds (-1) Warning: Frame 165 Coordinates out of bounds (-1) Warning: Frame 166 Coordinates out of bounds (-1) Warning: Frame 167 Coordinates out of bounds (-1) Warning: Frame 168 Coordinates out of bounds (-1) Warning: Frame 169 Coordinates out of bounds (-1) Warning: Frame 170 Coordinates out of bounds (-1) Warning: Frame 171 Coordinates out of bounds (-1) Warning: Frame 172 Coordinates out of bounds (-1) Warning: Frame 173 Coordinates out of bounds (-1) Warning: Frame 174 Coordinates out of bounds (-1) Warning: Frame 175 Coordinates out of bounds (-1) Warning: Frame 176 Coordinates out of bounds (-1) Warning: Frame 177 Coordinates out of bounds (-1) Warning: Frame 178 Coordinates out of bounds (-1) Warning: Frame 179 Coordinates out of bounds (-1) Warning: Frame 180 Coordinates out of bounds (-1) Warning: Frame 181 Coordinates out of bounds (-1) Warning: Frame 182 Coordinates out of bounds (-1) Warning: Frame 183 Coordinates out of bounds (-1) Warning: Frame 184 Coordinates out of bounds (-1) Warning: Frame 185 Coordinates out of bounds (-1) Warning: Frame 186 Coordinates out of bounds (-1) Warning: Frame 187 Coordinates out of bounds (-1) Warning: Frame 188 Coordinates out of bounds (-1) Warning: Frame 189 Coordinates out of bounds (-1) Warning: Frame 190 Coordinates out of bounds (-1) Warning: Frame 191 Coordinates out of bounds (-1) Warning: Frame 192 Coordinates out of bounds (-1) Warning: Frame 193 Coordinates out of bounds (-1) Warning: Frame 194 Coordinates out of bounds (-1) Warning: Frame 195 Coordinates out of bounds (-1) Warning: Frame 196 Coordinates out of bounds (-1) Warning: Frame 197 Coordinates out of bounds (-1) Warning: Frame 198 Coordinates out of bounds (-1) Warning: Frame 199 Coordinates out of bounds (-1) Warning: Frame 200 Coordinates out of bounds (-1) Warning: Frame 201 Coordinates out of bounds (-1) Warning: Frame 202 Coordinates out of bounds (-1) Warning: Frame 203 Coordinates out of bounds (-1) Warning: Frame 204 Coordinates out of bounds (-1) Warning: Frame 205 Coordinates out of bounds (-1) Warning: Frame 206 Coordinates out of bounds (-1) Warning: Frame 207 Coordinates out of bounds (-1) Warning: Frame 208 Coordinates out of bounds (-1) Warning: Frame 209 Coordinates out of bounds (-1) Warning: Frame 210 Coordinates out of bounds (-1) Warning: Frame 211 Coordinates out of bounds (-1) Warning: Frame 212 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 221 Coordinates out of bounds (-1) Warning: Frame 222 Coordinates out of bounds (-1) Warning: Frame 223 Coordinates out of bounds (-1) Warning: Frame 224 Coordinates out of bounds (-1) Warning: Frame 225 Coordinates out of bounds (-1) Warning: Frame 226 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 0.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 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: 226 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 226.000000 TIME: Analyses took 0.0014 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 226 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 226 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 226 COM "COM" (double, distance), size is 226 g1 "g1" (double, torsion(gamma)), size is 226 d1 "d1" (double, torsion(delta)), size is 226 e1 "e1" (double, torsion(epsilon)), size is 226 z1 "z1" (double, torsion(zeta)), size is 226 c1 "c1" (double, torsion(chi)), size is 226 a2 "a2" (double, torsion(alpha)), size is 226 b2 "b2" (double, torsion(beta)), size is 226 g2 "g2" (double, torsion(gamma)), size is 226 d2 "d2" (double, torsion(delta)), size is 226 c2 "c2" (double, torsion(chi)), size is 226 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: 0.0702 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.