CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:03:06 | Available memory: 1.737 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.c6] Reading '../ctraj.c6' 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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@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 (1 total): 0: noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1565 of 1565) Coordinate processing will occur on 1565 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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 8: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- ctraj.c6 (1-1565, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 1565 frames and processed 1565 frames. TIME: Avg. throughput= 99226.4773 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 1565 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 1565 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 1565 COM "COM" (double, distance), size is 1565 g1 "g1" (double, torsion(gamma)), size is 1565 d1 "d1" (double, torsion(delta)), size is 1565 e1 "e1" (double, torsion(epsilon)), size is 1565 z1 "z1" (double, torsion(zeta)), size is 1565 c1 "c1" (double, torsion(chin)), size is 1565 a2 "a2" (double, torsion(alpha)), size is 1565 b2 "b2" (double, torsion(beta)), size is 1565 g2 "g2" (double, torsion(gamma)), size is 1565 d2 "d2" (double, torsion(delta)), size is 1565 c2 "c2" (double, torsion(chin)), size is 1565 RUN TIMING: TIME: Init : 0.0000 s ( 0.29%) TIME: Trajectory Process : 0.0158 s ( 99.28%) TIME: Action Post : 0.0000 s ( 0.03%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.26%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0159 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, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1565 of 1565) Coordinate processing will occur on 1565 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c6 (1-1565, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 1565 frames and processed 1565 frames. TIME: Avg. throughput= 309594.4609 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: 1565 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 1565 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: 1565 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 3 Coordinates out of bounds (-1) Warning: Frame 8 Coordinates out of bounds (-1) Warning: Frame 9 Coordinates out of bounds (-1) Warning: Frame 19 Coordinates out of bounds (-1) Warning: Frame 20 Coordinates out of bounds (-1) Warning: Frame 23 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 47 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 62 Coordinates out of bounds (-1) Warning: Frame 65 Coordinates out of bounds (-1) Warning: Frame 66 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 78 Coordinates out of bounds (-1) Warning: Frame 80 Coordinates out of bounds (-1) Warning: Frame 82 Coordinates out of bounds (-1) Warning: Frame 83 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 104 Coordinates out of bounds (-1) Warning: Frame 105 Coordinates out of bounds (-1) Warning: Frame 106 Coordinates out of bounds (-1) Warning: Frame 109 Coordinates out of bounds (-1) Warning: Frame 119 Coordinates out of bounds (-1) Warning: Frame 120 Coordinates out of bounds (-1) Warning: Frame 125 Coordinates out of bounds (-1) Warning: Frame 126 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 147 Coordinates out of bounds (-1) Warning: Frame 148 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 157 Coordinates out of bounds (-1) Warning: Frame 164 Coordinates out of bounds (-1) Warning: Frame 165 Coordinates out of bounds (-1) Warning: Frame 169 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 181 Coordinates out of bounds (-1) Warning: Frame 182 Coordinates out of bounds (-1) Warning: Frame 183 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 206 Coordinates out of bounds (-1) Warning: Frame 207 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 218 Coordinates out of bounds (-1) Warning: Frame 219 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 226 Coordinates out of bounds (-1) Warning: Frame 227 Coordinates out of bounds (-1) Warning: Frame 230 Coordinates out of bounds (-1) Warning: Frame 231 Coordinates out of bounds (-1) Warning: Frame 234 Coordinates out of bounds (-1) Warning: Frame 241 Coordinates out of bounds (-1) Warning: Frame 247 Coordinates out of bounds (-1) Warning: Frame 248 Coordinates out of bounds (-1) Warning: Frame 250 Coordinates out of bounds (-1) Warning: Frame 251 Coordinates out of bounds (-1) Warning: Frame 252 Coordinates out of bounds (-1) Warning: Frame 253 Coordinates out of bounds (-1) Warning: Frame 265 Coordinates out of bounds (-1) Warning: Frame 266 Coordinates out of bounds (-1) Warning: Frame 267 Coordinates out of bounds (-1) Warning: Frame 270 Coordinates out of bounds (-1) Warning: Frame 271 Coordinates out of bounds (-1) Warning: Frame 272 Coordinates out of bounds (-1) Warning: Frame 273 Coordinates out of bounds (-1) Warning: Frame 278 Coordinates out of bounds (-1) Warning: Frame 279 Coordinates out of bounds (-1) Warning: Frame 280 Coordinates out of bounds (-1) Warning: Frame 281 Coordinates out of bounds (-1) Warning: Frame 282 Coordinates out of bounds (-1) Warning: Frame 283 Coordinates out of bounds (-1) Warning: Frame 284 Coordinates out of bounds (-1) Warning: Frame 285 Coordinates out of bounds (-1) Warning: Frame 286 Coordinates out of bounds (-1) Warning: Frame 287 Coordinates out of bounds (-1) Warning: Frame 288 Coordinates out of bounds (-1) Warning: Frame 289 Coordinates out of bounds (-1) Warning: Frame 290 Coordinates out of bounds (-1) Warning: Frame 291 Coordinates out of bounds (-1) Warning: Frame 293 Coordinates out of bounds (-1) Warning: Frame 294 Coordinates out of bounds (-1) Warning: Frame 295 Coordinates out of bounds (-1) Warning: Frame 296 Coordinates out of bounds (-1) Warning: Frame 297 Coordinates out of bounds (-1) Warning: Frame 298 Coordinates out of bounds (-1) Warning: Frame 302 Coordinates out of bounds (-1) Warning: Frame 309 Coordinates out of bounds (-1) Warning: Frame 310 Coordinates out of bounds (-1) Warning: Frame 311 Coordinates out of bounds (-1) Warning: Frame 312 Coordinates out of bounds (-1) Warning: Frame 313 Coordinates out of bounds (-1) Warning: Frame 324 Coordinates out of bounds (-1) Warning: Frame 336 Coordinates out of bounds (-1) Warning: Frame 337 Coordinates out of bounds (-1) Warning: Frame 338 Coordinates out of bounds (-1) Warning: Frame 339 Coordinates out of bounds (-1) Warning: Frame 341 Coordinates out of bounds (-1) Warning: Frame 342 Coordinates out of bounds (-1) Warning: Frame 343 Coordinates out of bounds (-1) Warning: Frame 359 Coordinates out of bounds (-1) Warning: Frame 360 Coordinates out of bounds (-1) Warning: Frame 372 Coordinates out of bounds (-1) Warning: Frame 373 Coordinates out of bounds (-1) Warning: Frame 374 Coordinates out of bounds (-1) Warning: Frame 375 Coordinates out of bounds (-1) Warning: Frame 376 Coordinates out of bounds (-1) Warning: Frame 379 Coordinates out of bounds (-1) Warning: Frame 380 Coordinates out of bounds (-1) Warning: Frame 381 Coordinates out of bounds (-1) Warning: Frame 386 Coordinates out of bounds (-1) Warning: Frame 387 Coordinates out of bounds (-1) Warning: Frame 388 Coordinates out of bounds (-1) Warning: Frame 389 Coordinates out of bounds (-1) Warning: Frame 390 Coordinates out of bounds (-1) Warning: Frame 391 Coordinates out of bounds (-1) Warning: Frame 392 Coordinates out of bounds (-1) Warning: Frame 393 Coordinates out of bounds (-1) Warning: Frame 394 Coordinates out of bounds (-1) Warning: Frame 395 Coordinates out of bounds (-1) Warning: Frame 396 Coordinates out of bounds (-1) Warning: Frame 397 Coordinates out of bounds (-1) Warning: Frame 398 Coordinates out of bounds (-1) Warning: Frame 399 Coordinates out of bounds (-1) Warning: Frame 400 Coordinates out of bounds (-1) Warning: Frame 401 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 409 Coordinates out of bounds (-1) Warning: Frame 411 Coordinates out of bounds (-1) Warning: Frame 415 Coordinates out of bounds (-1) Warning: Frame 420 Coordinates out of bounds (-1) Warning: Frame 423 Coordinates out of bounds (-1) Warning: Frame 424 Coordinates out of bounds (-1) Warning: Frame 425 Coordinates out of bounds (-1) Warning: Frame 426 Coordinates out of bounds (-1) Warning: Frame 427 Coordinates out of bounds (-1) Warning: Frame 434 Coordinates out of bounds (-1) Warning: Frame 439 Coordinates out of bounds (-1) Warning: Frame 440 Coordinates out of bounds (-1) Warning: Frame 441 Coordinates out of bounds (-1) Warning: Frame 442 Coordinates out of bounds (-1) Warning: Frame 443 Coordinates out of bounds (-1) Warning: Frame 444 Coordinates out of bounds (-1) Warning: Frame 447 Coordinates out of bounds (-1) Warning: Frame 455 Coordinates out of bounds (-1) Warning: Frame 456 Coordinates out of bounds (-1) Warning: Frame 457 Coordinates out of bounds (-1) Warning: Frame 459 Coordinates out of bounds (-1) Warning: Frame 460 Coordinates out of bounds (-1) Warning: Frame 461 Coordinates out of bounds (-1) Warning: Frame 463 Coordinates out of bounds (-1) Warning: Frame 465 Coordinates out of bounds (-1) Warning: Frame 472 Coordinates out of bounds (-1) Warning: Frame 494 Coordinates out of bounds (-1) Warning: Frame 499 Coordinates out of bounds (-1) Warning: Frame 500 Coordinates out of bounds (-1) Warning: Frame 501 Coordinates out of bounds (-1) Warning: Frame 502 Coordinates out of bounds (-1) Warning: Frame 503 Coordinates out of bounds (-1) Warning: Frame 504 Coordinates out of bounds (-1) Warning: Frame 505 Coordinates out of bounds (-1) Warning: Frame 509 Coordinates out of bounds (-1) Warning: Frame 510 Coordinates out of bounds (-1) Warning: Frame 512 Coordinates out of bounds (-1) Warning: Frame 514 Coordinates out of bounds (-1) Warning: Frame 515 Coordinates out of bounds (-1) Warning: Frame 517 Coordinates out of bounds (-1) Warning: Frame 539 Coordinates out of bounds (-1) Warning: Frame 546 Coordinates out of bounds (-1) Warning: Frame 552 Coordinates out of bounds (-1) Warning: Frame 553 Coordinates out of bounds (-1) Warning: Frame 554 Coordinates out of bounds (-1) Warning: Frame 555 Coordinates out of bounds (-1) Warning: Frame 556 Coordinates out of bounds (-1) Warning: Frame 563 Coordinates out of bounds (-1) Warning: Frame 568 Coordinates out of bounds (-1) Warning: Frame 569 Coordinates out of bounds (-1) Warning: Frame 570 Coordinates out of bounds (-1) Warning: Frame 579 Coordinates out of bounds (-1) Warning: Frame 583 Coordinates out of bounds (-1) Warning: Frame 584 Coordinates out of bounds (-1) Warning: Frame 589 Coordinates out of bounds (-1) Warning: Frame 590 Coordinates out of bounds (-1) Warning: Frame 593 Coordinates out of bounds (-1) Warning: Frame 595 Coordinates out of bounds (-1) Warning: Frame 597 Coordinates out of bounds (-1) Warning: Frame 601 Coordinates out of bounds (-1) Warning: Frame 602 Coordinates out of bounds (-1) Warning: Frame 605 Coordinates out of bounds (-1) Warning: Frame 606 Coordinates out of bounds (-1) Warning: Frame 607 Coordinates out of bounds (-1) Warning: Frame 608 Coordinates out of bounds (-1) Warning: Frame 609 Coordinates out of bounds (-1) Warning: Frame 611 Coordinates out of bounds (-1) Warning: Frame 613 Coordinates out of bounds (-1) Warning: Frame 623 Coordinates out of bounds (-1) Warning: Frame 624 Coordinates out of bounds (-1) Warning: Frame 625 Coordinates out of bounds (-1) Warning: Frame 626 Coordinates out of bounds (-1) Warning: Frame 627 Coordinates out of bounds (-1) Warning: Frame 628 Coordinates out of bounds (-1) Warning: Frame 632 Coordinates out of bounds (-1) Warning: Frame 636 Coordinates out of bounds (-1) Warning: Frame 639 Coordinates out of bounds (-1) Warning: Frame 644 Coordinates out of bounds (-1) Warning: Frame 645 Coordinates out of bounds (-1) Warning: Frame 650 Coordinates out of bounds (-1) Warning: Frame 655 Coordinates out of bounds (-1) Warning: Frame 659 Coordinates out of bounds (-1) Warning: Frame 661 Coordinates out of bounds (-1) Warning: Frame 662 Coordinates out of bounds (-1) Warning: Frame 664 Coordinates out of bounds (-1) Warning: Frame 665 Coordinates 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bounds (-1) Warning: Frame 1424 Coordinates out of bounds (-1) Warning: Frame 1433 Coordinates out of bounds (-1) Warning: Frame 1468 Coordinates out of bounds (-1) Warning: Frame 1477 Coordinates out of bounds (-1) Warning: Frame 1484 Coordinates out of bounds (-1) Warning: Frame 1488 Coordinates out of bounds (-1) Warning: Frame 1492 Coordinates out of bounds (-1) Warning: Frame 1493 Coordinates out of bounds (-1) Warning: Frame 1497 Coordinates out of bounds (-1) Warning: Frame 1503 Coordinates out of bounds (-1) Warning: Frame 1508 Coordinates out of bounds (-1) Warning: Frame 1519 Coordinates out of bounds (-1) Warning: Frame 1520 Coordinates out of bounds (-1) Warning: Frame 1522 Coordinates out of bounds (-1) Warning: Frame 1523 Coordinates out of bounds (-1) Warning: Frame 1524 Coordinates out of bounds (-1) Warning: Frame 1526 Coordinates out of bounds (-1) Warning: Frame 1527 Coordinates out of bounds (-1) Warning: Frame 1528 Coordinates out of bounds (-1) Warning: Frame 1529 Coordinates out of bounds (-1) Warning: Frame 1543 Coordinates out of bounds (-1) Warning: Frame 1545 Coordinates out of bounds (-1) Warning: Frame 1546 Coordinates out of bounds (-1) Warning: Frame 1547 Coordinates out of bounds (-1) Warning: Frame 1548 Coordinates out of bounds (-1) Warning: Frame 1549 Coordinates out of bounds (-1) Warning: Frame 1550 Coordinates out of bounds (-1) Warning: Frame 1555 Coordinates out of bounds (-1) Warning: Frame 1556 Coordinates out of bounds (-1) Warning: Frame 1557 Coordinates out of bounds (-1) Warning: Frame 1558 Coordinates out of bounds (-1) Warning: Frame 1560 Coordinates out of bounds (-1) Warning: Frame 1562 Coordinates out of bounds (-1) Warning: Frame 1564 Coordinates out of bounds (-1) Warning: Frame 1565 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 914 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 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: 1565 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 1565 TIME: Analyses took 0.0011 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 1565 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 1565 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 1565 COM "COM" (double, distance), size is 1565 g1 "g1" (double, torsion(gamma)), size is 1565 d1 "d1" (double, torsion(delta)), size is 1565 e1 "e1" (double, torsion(epsilon)), size is 1565 z1 "z1" (double, torsion(zeta)), size is 1565 c1 "c1" (double, torsion(chin)), size is 1565 a2 "a2" (double, torsion(alpha)), size is 1565 b2 "b2" (double, torsion(beta)), size is 1565 g2 "g2" (double, torsion(gamma)), size is 1565 d2 "d2" (double, torsion(delta)), size is 1565 c2 "c2" (double, torsion(chin)), size is 1565 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 ( 0.08%) TIME: Trajectory Process : 0.0051 s ( 14.73%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0011 s ( 3.25%) TIME: Data File Write : 0.0281 s ( 81.87%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0343 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0640 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.