CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:34:59 | Available memory: 53201.9 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.c4] Reading '../ctraj.c4' 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*](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 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', 67 atoms, 2 res, box: Orthogonal, 1 mol, 32990 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 32990 of 32990) Coordinate processing will occur on 32990 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*](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 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.c4 (1-32990, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 32990 frames and processed 32990 frames. TIME: Trajectory processing: 0.1322 s TIME: Avg. throughput= 249576.3481 frames / second. ACTION OUTPUT: DATASETS: 15 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (67 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 32990 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 32990 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 32990 COM "COM" (double, distance), size is 32990 g1 "g1" (double, torsion(gamma)), size is 32990 d1 "d1" (double, torsion(delta)), size is 32990 e1 "e1" (double, torsion(epsilon)), size is 32990 z1 "z1" (double, torsion(zeta)), size is 32990 c1 "c1" (double, torsion(chi)), size is 32990 a2 "a2" (double, torsion(alpha)), size is 32990 b2 "b2" (double, torsion(beta)), size is 32990 g2 "g2" (double, torsion(gamma)), size is 32990 d2 "d2" (double, torsion(delta)), size is 32990 c2 "c2" (double, torsion(chi)), size is 32990 ---------- 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: 32990 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 32990.000000 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: 32990 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 75 Coordinates out of bounds (-1) Warning: Frame 79 Coordinates out of bounds (-1) Warning: Frame 80 Coordinates out of bounds (-1) Warning: Frame 197 Coordinates out of bounds (-1) Warning: Frame 242 Coordinates out of bounds (-1) Warning: Frame 372 Coordinates out of bounds (-1) Warning: Frame 607 Coordinates out of bounds (-1) Warning: Frame 610 Coordinates out of bounds (-1) Warning: Frame 614 Coordinates out of bounds (-1) Warning: Frame 639 Coordinates out of bounds (-1) Warning: Frame 642 Coordinates out of bounds (-1) Warning: Frame 645 Coordinates out of bounds (-1) Warning: Frame 655 Coordinates out of bounds (-1) Warning: Frame 788 Coordinates out of bounds (-1) Warning: Frame 1128 Coordinates out of bounds (-1) Warning: Frame 1211 Coordinates out of bounds (-1) Warning: Frame 1220 Coordinates out of bounds (-1) Warning: Frame 1232 Coordinates out of bounds (-1) Warning: Frame 1306 Coordinates out of bounds (-1) Warning: Frame 1326 Coordinates out of bounds (-1) Warning: Frame 1436 Coordinates out of bounds (-1) Warning: Frame 1447 Coordinates out of bounds (-1) Warning: Frame 1565 Coordinates out of bounds (-1) Warning: Frame 1578 Coordinates out of bounds (-1) Warning: Frame 1614 Coordinates out of bounds (-1) Warning: Frame 1788 Coordinates out of bounds (-1) Warning: Frame 1988 Coordinates out of bounds (-1) Warning: Frame 2136 Coordinates out of bounds (-1) Warning: Frame 2141 Coordinates out of bounds (-1) Warning: Frame 2144 Coordinates out of bounds (-1) Warning: Frame 2188 Coordinates out of bounds (-1) Warning: Frame 2430 Coordinates out of bounds (-1) Warning: Frame 2577 Coordinates out of bounds (-1) Warning: Frame 2578 Coordinates out of bounds (-1) Warning: Frame 2583 Coordinates out of bounds (-1) Warning: Frame 2584 Coordinates out of bounds (-1) Warning: Frame 2690 Coordinates out of bounds (-1) Warning: Frame 2943 Coordinates out of bounds (-1) Warning: Frame 3190 Coordinates out of bounds (-1) Warning: Frame 3279 Coordinates out of bounds (-1) Warning: Frame 3291 Coordinates out of bounds (-1) Warning: Frame 3329 Coordinates out of bounds (-1) Warning: Frame 3372 Coordinates out of bounds (-1) Warning: Frame 3373 Coordinates out of bounds (-1) Warning: Frame 3502 Coordinates out of bounds (-1) Warning: Frame 3866 Coordinates out of bounds (-1) Warning: Frame 3974 Coordinates out of bounds (-1) Warning: Frame 4003 Coordinates out of bounds (-1) Warning: Frame 4083 Coordinates out of bounds (-1) Warning: Frame 4146 Coordinates out of bounds (-1) Warning: Frame 4147 Coordinates out of bounds (-1) Warning: Frame 4237 Coordinates out of bounds (-1) Warning: Frame 4305 Coordinates out of bounds (-1) Warning: Frame 4306 Coordinates out of bounds (-1) Warning: Frame 4385 Coordinates out of bounds (-1) Warning: Frame 4741 Coordinates out of bounds (-1) Warning: Frame 4805 Coordinates out of bounds (-1) Warning: Frame 4958 Coordinates out of bounds (-1) Warning: 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bounds (-1) Warning: Frame 6448 Coordinates out of bounds (-1) Warning: Frame 6454 Coordinates out of bounds (-1) Warning: Frame 6455 Coordinates out of bounds (-1) Warning: Frame 6523 Coordinates out of bounds (-1) Warning: Frame 6574 Coordinates out of bounds (-1) Warning: Frame 6754 Coordinates out of bounds (-1) Warning: Frame 6816 Coordinates out of bounds (-1) Warning: Frame 6896 Coordinates out of bounds (-1) Warning: Frame 7250 Coordinates out of bounds (-1) Warning: Frame 7252 Coordinates out of bounds (-1) Warning: Frame 7254 Coordinates out of bounds (-1) Warning: Frame 7516 Coordinates out of bounds (-1) Warning: Frame 7617 Coordinates out of bounds (-1) Warning: Frame 7853 Coordinates out of bounds (-1) Warning: Frame 7896 Coordinates out of bounds (-1) Warning: Frame 7898 Coordinates out of bounds (-1) Warning: Frame 7903 Coordinates out of bounds (-1) Warning: Frame 8019 Coordinates out of bounds (-1) Warning: Frame 8038 Coordinates out of bounds (-1) Warning: Frame 8052 Coordinates out of bounds (-1) Warning: Frame 8107 Coordinates out of bounds (-1) Warning: Frame 8109 Coordinates out of bounds (-1) Warning: Frame 8123 Coordinates out of bounds (-1) Warning: Frame 8244 Coordinates out of bounds (-1) Warning: Frame 8574 Coordinates out of bounds (-1) Warning: Frame 8597 Coordinates out of bounds (-1) Warning: Frame 8784 Coordinates out of bounds (-1) Warning: Frame 8841 Coordinates out of bounds (-1) Warning: Frame 9012 Coordinates out of bounds (-1) Warning: Frame 9030 Coordinates out of bounds (-1) Warning: Frame 9440 Coordinates out of bounds (-1) Warning: Frame 9517 Coordinates out of bounds (-1) Warning: Frame 9553 Coordinates out of bounds (-1) Warning: Frame 9602 Coordinates out of bounds (-1) Warning: Frame 9629 Coordinates out of bounds (-1) Warning: Frame 9654 Coordinates out of bounds (-1) Warning: Frame 9933 Coordinates out of bounds (-1) Warning: Frame 10013 Coordinates out of bounds (-1) Warning: Frame 10015 Coordinates out of bounds (-1) Warning: Frame 10037 Coordinates out of bounds (-1) Warning: Frame 10054 Coordinates out of bounds (-1) Warning: Frame 10304 Coordinates out of bounds (-1) Warning: Frame 10305 Coordinates out of bounds (-1) Warning: Frame 10728 Coordinates out of bounds (-1) Warning: Frame 10830 Coordinates out of bounds (-1) Warning: Frame 10902 Coordinates out of bounds (-1) Warning: Frame 11096 Coordinates out of bounds (-1) Warning: Frame 11155 Coordinates out of bounds (-1) Warning: Frame 11236 Coordinates out of bounds (-1) Warning: Frame 11641 Coordinates out of bounds (-1) Warning: Frame 11843 Coordinates out of bounds (-1) Warning: Frame 12262 Coordinates out of bounds (-1) Warning: Frame 12265 Coordinates out of bounds (-1) Warning: Frame 12367 Coordinates out of bounds (-1) Warning: Frame 12377 Coordinates out of bounds (-1) Warning: Frame 12392 Coordinates out of bounds (-1) Warning: Frame 12419 Coordinates out of bounds (-1) Warning: Frame 12491 Coordinates out of bounds (-1) Warning: Frame 12521 Coordinates out of bounds (-1) Warning: Frame 12529 Coordinates out of bounds (-1) Warning: Frame 12542 Coordinates out of bounds (-1) Warning: Frame 12543 Coordinates out of bounds (-1) Warning: Frame 12544 Coordinates out of bounds (-1) Warning: Frame 12596 Coordinates out of bounds (-1) Warning: Frame 12607 Coordinates out of bounds (-1) Warning: Frame 12608 Coordinates out of bounds (-1) Warning: Frame 12627 Coordinates out of bounds (-1) Warning: Frame 12628 Coordinates out of bounds (-1) Warning: Frame 12642 Coordinates out of bounds (-1) Warning: Frame 12711 Coordinates out of bounds (-1) Warning: Frame 12774 Coordinates out of bounds (-1) Warning: Frame 12775 Coordinates out of bounds (-1) Warning: Frame 12804 Coordinates out of bounds (-1) Warning: Frame 12823 Coordinates out of bounds (-1) Warning: Frame 12824 Coordinates out of bounds (-1) Warning: Frame 12827 Coordinates out of bounds (-1) Warning: Frame 12864 Coordinates out of bounds (-1) Warning: Frame 12883 Coordinates out of bounds (-1) Warning: Frame 12996 Coordinates out of bounds (-1) Warning: Frame 13026 Coordinates out of bounds (-1) Warning: Frame 13060 Coordinates out of bounds (-1) Warning: Frame 13063 Coordinates out of bounds (-1) Warning: Frame 13102 Coordinates out of bounds (-1) Warning: Frame 13124 Coordinates out of bounds (-1) Warning: Frame 13131 Coordinates out of bounds (-1) Warning: Frame 13168 Coordinates out of bounds (-1) Warning: Frame 13205 Coordinates out of bounds (-1) Warning: Frame 13233 Coordinates out of bounds (-1) Warning: Frame 13235 Coordinates out of bounds (-1) Warning: Frame 13239 Coordinates out of bounds (-1) Warning: Frame 13345 Coordinates out of bounds (-1) Warning: Frame 13357 Coordinates out of bounds (-1) Warning: Frame 13368 Coordinates out of bounds (-1) Warning: Frame 13370 Coordinates out of bounds (-1) Warning: Frame 13479 Coordinates out of bounds (-1) Warning: Frame 13575 Coordinates out of bounds (-1) Warning: Frame 13581 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out of bounds (-1) Warning: Frame 14096 Coordinates out of bounds (-1) Warning: Frame 14144 Coordinates out of bounds (-1) Warning: Frame 14147 Coordinates out of bounds (-1) Warning: Frame 14213 Coordinates out of bounds (-1) Warning: Frame 14214 Coordinates out of bounds (-1) Warning: Frame 14221 Coordinates out of bounds (-1) Warning: Frame 14276 Coordinates out of bounds (-1) Warning: Frame 14334 Coordinates out of bounds (-1) Warning: Frame 14394 Coordinates out of bounds (-1) Warning: Frame 14403 Coordinates out of bounds (-1) Warning: Frame 14454 Coordinates out of bounds (-1) Warning: Frame 14461 Coordinates out of bounds (-1) Warning: Frame 14570 Coordinates out of bounds (-1) Warning: Frame 14619 Coordinates out of bounds (-1) Warning: Frame 14620 Coordinates out of bounds (-1) Warning: Frame 14677 Coordinates out of bounds (-1) Warning: Frame 14692 Coordinates out of bounds (-1) Warning: Frame 14727 Coordinates out of bounds (-1) Warning: Frame 14789 Coordinates out of bounds (-1) Warning: Frame 14835 Coordinates out of bounds (-1) Warning: Frame 14853 Coordinates out of bounds (-1) Warning: Frame 14914 Coordinates out of bounds (-1) Warning: Frame 14916 Coordinates out of bounds (-1) Warning: Frame 14920 Coordinates out of bounds (-1) Warning: Frame 15045 Coordinates out of bounds (-1) Warning: Frame 15048 Coordinates out of bounds (-1) Warning: Frame 15061 Coordinates out of bounds (-1) Warning: Frame 15064 Coordinates out of bounds (-1) Warning: Frame 15203 Coordinates out of bounds (-1) Warning: Frame 15221 Coordinates out of bounds (-1) Warning: Frame 15222 Coordinates out of bounds (-1) Warning: Frame 15237 Coordinates out of bounds (-1) Warning: Frame 15378 Coordinates out of bounds (-1) Warning: Frame 15408 Coordinates out of bounds (-1) Warning: Frame 15409 Coordinates out of bounds (-1) Warning: Frame 15434 Coordinates out of bounds (-1) Warning: Frame 15449 Coordinates out of bounds (-1) Warning: Frame 15471 Coordinates out of bounds (-1) Warning: Frame 15573 Coordinates out of bounds (-1) Warning: Frame 15574 Coordinates out of bounds (-1) Warning: Frame 15596 Coordinates out of bounds (-1) Warning: Frame 15605 Coordinates out of bounds (-1) Warning: Frame 15606 Coordinates out of bounds (-1) Warning: Frame 15641 Coordinates out of bounds (-1) Warning: Frame 15718 Coordinates out of bounds (-1) Warning: Frame 15789 Coordinates out of bounds (-1) Warning: Frame 15802 Coordinates out of bounds (-1) Warning: Frame 15803 Coordinates out of bounds (-1) Warning: Frame 15843 Coordinates out of bounds (-1) Warning: Frame 15865 Coordinates out of bounds (-1) Warning: Frame 15905 Coordinates out of bounds (-1) Warning: Frame 15906 Coordinates out of bounds (-1) Warning: Frame 15961 Coordinates out of bounds (-1) Warning: Frame 15962 Coordinates out of bounds (-1) Warning: Frame 15963 Coordinates out of bounds (-1) Warning: Frame 15988 Coordinates out of bounds (-1) Warning: Frame 15990 Coordinates out of bounds (-1) Warning: 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out of bounds (-1) Warning: Frame 22172 Coordinates out of bounds (-1) Warning: Frame 22173 Coordinates out of bounds (-1) Warning: Frame 22184 Coordinates out of bounds (-1) Warning: Frame 22199 Coordinates out of bounds (-1) Warning: Frame 22204 Coordinates out of bounds (-1) Warning: Frame 22227 Coordinates out of bounds (-1) Warning: Frame 22242 Coordinates out of bounds (-1) Warning: Frame 22243 Coordinates out of bounds (-1) Warning: Frame 22260 Coordinates out of bounds (-1) Warning: Frame 22264 Coordinates out of bounds (-1) Warning: Frame 22267 Coordinates out of bounds (-1) Warning: Frame 22295 Coordinates out of bounds (-1) Warning: Frame 22296 Coordinates out of bounds (-1) Warning: Frame 22329 Coordinates out of bounds (-1) Warning: Frame 22338 Coordinates out of bounds (-1) Warning: Frame 22353 Coordinates out of bounds (-1) Warning: Frame 22360 Coordinates out of bounds (-1) Warning: Frame 22373 Coordinates out of bounds (-1) Warning: Frame 22374 Coordinates out of bounds (-1) Warning: Frame 22375 Coordinates out of bounds (-1) Warning: Frame 22381 Coordinates out of bounds (-1) Warning: Frame 22389 Coordinates out of bounds (-1) Warning: Frame 22401 Coordinates out of bounds (-1) Warning: Frame 22402 Coordinates out of bounds (-1) Warning: Frame 22411 Coordinates out of bounds (-1) Warning: Frame 22415 Coordinates out of bounds (-1) Warning: Frame 22420 Coordinates out of bounds (-1) Warning: Frame 22430 Coordinates out of bounds (-1) Warning: Frame 22440 Coordinates out of bounds (-1) Warning: Frame 22451 Coordinates out of bounds (-1) Warning: Frame 22460 Coordinates out of bounds (-1) Warning: Frame 22468 Coordinates out of bounds (-1) Warning: Frame 22474 Coordinates out of bounds (-1) Warning: Frame 22488 Coordinates out of bounds (-1) Warning: Frame 22490 Coordinates out of bounds (-1) Warning: Frame 22496 Coordinates out of bounds (-1) Warning: Frame 22503 Coordinates out of bounds (-1) Warning: Frame 22504 Coordinates out of bounds (-1) 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Coordinates out of bounds (-1) Warning: Frame 26801 Coordinates out of bounds (-1) Warning: Frame 26840 Coordinates out of bounds (-1) Warning: Frame 27242 Coordinates out of bounds (-1) Warning: Frame 27245 Coordinates out of bounds (-1) Warning: Frame 27536 Coordinates out of bounds (-1) Warning: Frame 27617 Coordinates out of bounds (-1) Warning: Frame 27668 Coordinates out of bounds (-1) Warning: Frame 27921 Coordinates out of bounds (-1) Warning: Frame 27983 Coordinates out of bounds (-1) Warning: Frame 28139 Coordinates out of bounds (-1) Warning: Frame 28149 Coordinates out of bounds (-1) Warning: Frame 28178 Coordinates out of bounds (-1) Warning: Frame 28260 Coordinates out of bounds (-1) Warning: Frame 28375 Coordinates out of bounds (-1) Warning: Frame 28389 Coordinates out of bounds (-1) Warning: Frame 28390 Coordinates out of bounds (-1) Warning: Frame 28575 Coordinates out of bounds (-1) Warning: Frame 28622 Coordinates out of bounds (-1) Warning: Frame 28650 Coordinates out of bounds (-1) Warning: Frame 28832 Coordinates out of bounds (-1) Warning: Frame 28874 Coordinates out of bounds (-1) Warning: Frame 28912 Coordinates out of bounds (-1) Warning: Frame 29062 Coordinates out of bounds (-1) Warning: Frame 29114 Coordinates out of bounds (-1) Warning: Frame 29115 Coordinates out of bounds (-1) Warning: Frame 29379 Coordinates out of bounds (-1) Warning: Frame 29425 Coordinates out of bounds (-1) Warning: Frame 29456 Coordinates out of bounds (-1) Warning: Frame 29457 Coordinates out of bounds (-1) Warning: Frame 29890 Coordinates out of bounds (-1) Warning: Frame 30016 Coordinates out of bounds (-1) Warning: Frame 30114 Coordinates out of bounds (-1) Warning: Frame 30115 Coordinates out of bounds (-1) Warning: Frame 30190 Coordinates out of bounds (-1) Warning: Frame 30566 Coordinates out of bounds (-1) Warning: Frame 30838 Coordinates out of bounds (-1) Warning: Frame 30883 Coordinates out of bounds (-1) Warning: Frame 30884 Coordinates out of bounds (-1) Warning: Frame 31178 Coordinates out of bounds (-1) Warning: Frame 31226 Coordinates out of bounds (-1) Warning: Frame 31228 Coordinates out of bounds (-1) Warning: Frame 31311 Coordinates out of bounds (-1) Warning: Frame 31312 Coordinates out of bounds (-1) Warning: Frame 31469 Coordinates out of bounds (-1) Warning: Frame 31486 Coordinates out of bounds (-1) Warning: Frame 31487 Coordinates out of bounds (-1) Warning: Frame 31488 Coordinates out of bounds (-1) Warning: Frame 31497 Coordinates out of bounds (-1) Warning: Frame 31498 Coordinates out of bounds (-1) Warning: Frame 31500 Coordinates out of bounds (-1) Warning: Frame 31578 Coordinates out of bounds (-1) Warning: Frame 31579 Coordinates out of bounds (-1) Warning: Frame 32092 Coordinates out of bounds (-1) Warning: Frame 32274 Coordinates out of bounds (-1) Warning: Frame 32371 Coordinates out of bounds (-1) Warning: Frame 32813 Coordinates out of bounds (-1) Warning: Frame 32814 Coordinates out of bounds (-1) Warning: Frame 32815 Coordinates out of bounds (-1) Warning: Frame 32816 Coordinates out of bounds (-1) Warning: Frame 32817 Coordinates out of bounds (-1) Warning: Frame 32943 Coordinates out of bounds (-1) Warning: Frame 32945 Coordinates out of bounds (-1) Warning: Frame 32946 Coordinates out of bounds (-1) Warning: Frame 32947 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 32271.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 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: 32990 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 32990.000000 TIME: Analyses took 0.0049 seconds. DATASETS: 30 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb', refindex 0 (67 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 32990 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 32990 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 32990 COM "COM" (double, distance), size is 32990 g1 "g1" (double, torsion(gamma)), size is 32990 d1 "d1" (double, torsion(delta)), size is 32990 e1 "e1" (double, torsion(epsilon)), size is 32990 z1 "z1" (double, torsion(zeta)), size is 32990 c1 "c1" (double, torsion(chi)), size is 32990 a2 "a2" (double, torsion(alpha)), size is 32990 b2 "b2" (double, torsion(beta)), size is 32990 g2 "g2" (double, torsion(gamma)), size is 32990 d2 "d2" (double, torsion(delta)), size is 32990 c2 "c2" (double, torsion(chi)), size is 32990 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: 0.2205 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.