CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:33:15 | Available memory: 3.487 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.c3] Reading '../ctraj.c3' 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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,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@N1 :2@C2 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5081 of 5081) Coordinate processing will occur on 5081 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*](37) Reference mask: [:1,2&!@H*](37) 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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@N1 :2@C2 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c3 (1-5081, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5081 frames and processed 5081 frames. TIME: Avg. throughput= 110121.3697 frames / second. ACTION OUTPUT: DATASETS (14 total): rms_2_aform "rms_2_aform" (double, rms), size is 5081 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 5081 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 5081 COM "COM" (double, distance), size is 5081 g1 "g1" (double, torsion(gamma)), size is 5081 d1 "d1" (double, torsion(delta)), size is 5081 e1 "e1" (double, torsion(epsilon)), size is 5081 z1 "z1" (double, torsion(zeta)), size is 5081 c1 "c1" (double, torsion(chin)), size is 5081 a2 "a2" (double, torsion(alpha)), size is 5081 b2 "b2" (double, torsion(beta)), size is 5081 g2 "g2" (double, torsion(gamma)), size is 5081 d2 "d2" (double, torsion(delta)), size is 5081 c2 "c2" (double, torsion(chin)), size is 5081 RUN TIMING: TIME: Init : 0.0000 s ( 0.09%) TIME: Trajectory Process : 0.0461 s ( 99.77%) TIME: Action Post : 0.0000 s ( 0.01%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.08%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0462 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, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5081 of 5081) Coordinate processing will occur on 5081 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c3 (1-5081, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5081 frames and processed 5081 frames. TIME: Avg. throughput= 464867.3376 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: 5081 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 5081 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: 5081 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 26 Coordinates out of bounds (-1) Warning: Frame 41 Coordinates out of bounds (-1) Warning: Frame 45 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 85 Coordinates out of bounds (-1) Warning: Frame 86 Coordinates out of bounds (-1) Warning: Frame 87 Coordinates out of bounds (-1) Warning: Frame 93 Coordinates out of bounds (-1) Warning: Frame 94 Coordinates out of bounds (-1) Warning: Frame 96 Coordinates out of bounds (-1) Warning: Frame 108 Coordinates out of bounds (-1) Warning: Frame 118 Coordinates out of bounds (-1) Warning: Frame 128 Coordinates out of bounds (-1) Warning: Frame 132 Coordinates out of bounds (-1) Warning: Frame 135 Coordinates out of bounds (-1) Warning: Frame 136 Coordinates out of bounds (-1) Warning: Frame 140 Coordinates out of bounds (-1) Warning: Frame 151 Coordinates out of bounds (-1) Warning: Frame 153 Coordinates out of bounds (-1) Warning: Frame 154 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 176 Coordinates out of bounds (-1) Warning: Frame 177 Coordinates out of bounds (-1) Warning: Frame 186 Coordinates out of bounds (-1) Warning: Frame 206 Coordinates out of bounds (-1) Warning: Frame 219 Coordinates out of bounds (-1) Warning: Frame 223 Coordinates out of bounds (-1) Warning: Frame 233 Coordinates out of bounds (-1) Warning: Frame 238 Coordinates out of bounds (-1) Warning: Frame 239 Coordinates out of bounds (-1) Warning: Frame 240 Coordinates out of bounds (-1) Warning: Frame 241 Coordinates out of bounds (-1) Warning: Frame 252 Coordinates out of bounds (-1) Warning: Frame 264 Coordinates out of bounds (-1) Warning: Frame 266 Coordinates out of bounds (-1) Warning: Frame 271 Coordinates out of bounds (-1) Warning: Frame 272 Coordinates out of bounds (-1) Warning: Frame 276 Coordinates out of bounds (-1) Warning: Frame 281 Coordinates out of bounds (-1) Warning: Frame 319 Coordinates out of bounds (-1) Warning: Frame 322 Coordinates out of bounds (-1) Warning: Frame 323 Coordinates out of bounds (-1) Warning: Frame 324 Coordinates out of bounds (-1) Warning: Frame 325 Coordinates out of bounds (-1) Warning: Frame 336 Coordinates out of bounds (-1) Warning: Frame 342 Coordinates out of bounds (-1) Warning: Frame 349 Coordinates out of bounds (-1) Warning: Frame 356 Coordinates out of bounds (-1) Warning: Frame 377 Coordinates out of bounds (-1) Warning: Frame 384 Coordinates out of bounds (-1) Warning: Frame 385 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 395 Coordinates out of bounds (-1) Warning: Frame 396 Coordinates out of bounds (-1) Warning: Frame 442 Coordinates out of bounds (-1) Warning: Frame 465 Coordinates out of bounds (-1) Warning: Frame 466 Coordinates out of bounds (-1) Warning: Frame 468 Coordinates out of bounds (-1) Warning: Frame 475 Coordinates out of bounds (-1) Warning: Frame 486 Coordinates out of bounds (-1) Warning: Frame 491 Coordinates out of bounds (-1) Warning: Frame 493 Coordinates out of bounds (-1) Warning: Frame 514 Coordinates out of bounds (-1) Warning: Frame 530 Coordinates out of bounds (-1) Warning: Frame 532 Coordinates out of bounds (-1) Warning: Frame 543 Coordinates out of bounds (-1) Warning: Frame 549 Coordinates out of bounds (-1) Warning: Frame 553 Coordinates out of bounds (-1) Warning: Frame 561 Coordinates out of bounds (-1) Warning: Frame 591 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 609 Coordinates out of bounds (-1) Warning: Frame 610 Coordinates out of bounds (-1) Warning: Frame 615 Coordinates out of bounds (-1) Warning: Frame 620 Coordinates out of bounds (-1) Warning: Frame 630 Coordinates out of bounds (-1) Warning: Frame 632 Coordinates out of bounds (-1) Warning: Frame 651 Coordinates out of bounds (-1) Warning: Frame 655 Coordinates out of bounds (-1) Warning: Frame 673 Coordinates out of bounds (-1) Warning: Frame 677 Coordinates out of bounds (-1) Warning: Frame 678 Coordinates out of bounds (-1) Warning: Frame 679 Coordinates out of bounds (-1) Warning: Frame 686 Coordinates out of bounds (-1) Warning: Frame 687 Coordinates out of bounds (-1) Warning: Frame 717 Coordinates out of bounds (-1) Warning: Frame 736 Coordinates out of bounds (-1) Warning: Frame 747 Coordinates out of bounds (-1) Warning: Frame 752 Coordinates out of bounds (-1) Warning: Frame 761 Coordinates out of bounds (-1) Warning: Frame 768 Coordinates out of bounds (-1) Warning: Frame 775 Coordinates out of bounds (-1) Warning: Frame 777 Coordinates out of bounds (-1) Warning: Frame 788 Coordinates out of bounds (-1) Warning: Frame 802 Coordinates out of bounds (-1) Warning: Frame 803 Coordinates out of bounds (-1) Warning: Frame 817 Coordinates out of bounds (-1) Warning: Frame 822 Coordinates out of bounds (-1) Warning: Frame 824 Coordinates out of bounds (-1) Warning: Frame 830 Coordinates out of bounds (-1) Warning: Frame 832 Coordinates out of bounds (-1) Warning: Frame 841 Coordinates out of bounds (-1) Warning: Frame 849 Coordinates out of bounds (-1) Warning: Frame 853 Coordinates out of bounds (-1) Warning: Frame 854 Coordinates out of bounds (-1) Warning: Frame 883 Coordinates out of bounds (-1) Warning: Frame 885 Coordinates out of bounds (-1) Warning: Frame 888 Coordinates out of bounds (-1) Warning: Frame 905 Coordinates out of bounds (-1) Warning: Frame 906 Coordinates out of bounds (-1) Warning: Frame 907 Coordinates out of bounds (-1) Warning: Frame 910 Coordinates out of bounds (-1) Warning: Frame 911 Coordinates out of bounds (-1) Warning: Frame 912 Coordinates out of bounds (-1) Warning: Frame 916 Coordinates out of bounds (-1) Warning: Frame 965 Coordinates out of bounds (-1) Warning: Frame 981 Coordinates out of bounds (-1) Warning: Frame 982 Coordinates out of bounds (-1) Warning: Frame 983 Coordinates out of bounds (-1) Warning: Frame 984 Coordinates out of bounds (-1) Warning: Frame 985 Coordinates out of bounds (-1) Warning: Frame 988 Coordinates out of bounds (-1) Warning: Frame 990 Coordinates out of bounds (-1) Warning: Frame 993 Coordinates out of bounds (-1) Warning: Frame 1019 Coordinates out of bounds (-1) Warning: Frame 1034 Coordinates out of bounds (-1) Warning: Frame 1035 Coordinates out of bounds (-1) Warning: Frame 1036 Coordinates out of bounds (-1) Warning: Frame 1038 Coordinates out of bounds (-1) Warning: Frame 1040 Coordinates out of bounds (-1) Warning: Frame 1043 Coordinates out of bounds (-1) Warning: Frame 1060 Coordinates out of bounds (-1) Warning: Frame 1061 Coordinates out of bounds (-1) Warning: Frame 1063 Coordinates out of bounds (-1) Warning: Frame 1064 Coordinates out of bounds (-1) Warning: Frame 1065 Coordinates out of bounds (-1) Warning: Frame 1066 Coordinates out of bounds (-1) Warning: Frame 1071 Coordinates out of bounds (-1) Warning: Frame 1072 Coordinates out of bounds (-1) Warning: Frame 1079 Coordinates out of bounds (-1) Warning: Frame 1080 Coordinates out of bounds (-1) Warning: Frame 1081 Coordinates out of bounds (-1) Warning: Frame 1086 Coordinates out of bounds (-1) Warning: Frame 1091 Coordinates out of bounds (-1) Warning: Frame 1095 Coordinates out of bounds (-1) Warning: Frame 1096 Coordinates out of bounds (-1) Warning: Frame 1097 Coordinates out of bounds (-1) Warning: Frame 1109 Coordinates out of bounds (-1) Warning: Frame 1110 Coordinates out of bounds (-1) Warning: Frame 1140 Coordinates out of bounds (-1) Warning: Frame 1141 Coordinates out of bounds (-1) Warning: Frame 1154 Coordinates out of bounds (-1) Warning: Frame 1164 Coordinates out of bounds (-1) Warning: Frame 1167 Coordinates out of bounds (-1) Warning: Frame 1184 Coordinates out of bounds (-1) Warning: Frame 1191 Coordinates out of bounds (-1) Warning: Frame 1240 Coordinates out of bounds (-1) Warning: Frame 1242 Coordinates out of bounds (-1) Warning: Frame 1244 Coordinates out of bounds (-1) Warning: Frame 1247 Coordinates out of bounds (-1) Warning: Frame 1248 Coordinates out of bounds (-1) Warning: Frame 1260 Coordinates out of bounds (-1) Warning: Frame 1261 Coordinates out of bounds (-1) Warning: Frame 1266 Coordinates out of bounds (-1) Warning: Frame 1273 Coordinates out of bounds (-1) Warning: Frame 1279 Coordinates out of bounds (-1) Warning: Frame 1299 Coordinates out of bounds (-1) Warning: Frame 1300 Coordinates out of bounds (-1) Warning: Frame 1310 Coordinates out of bounds (-1) Warning: Frame 1324 Coordinates out of bounds (-1) Warning: Frame 1340 Coordinates out of bounds (-1) Warning: Frame 1342 Coordinates out of bounds (-1) Warning: Frame 1344 Coordinates out of bounds (-1) Warning: Frame 1345 Coordinates out of bounds (-1) Warning: Frame 1346 Coordinates out of bounds (-1) Warning: Frame 1359 Coordinates out of bounds (-1) Warning: Frame 1387 Coordinates out of bounds (-1) Warning: Frame 1398 Coordinates out of bounds (-1) Warning: Frame 1400 Coordinates out of bounds (-1) Warning: Frame 1424 Coordinates out of bounds (-1) Warning: Frame 1425 Coordinates out of bounds (-1) Warning: Frame 1435 Coordinates out of bounds (-1) Warning: Frame 1438 Coordinates out of bounds (-1) Warning: Frame 1440 Coordinates out of bounds (-1) Warning: Frame 1456 Coordinates out of bounds (-1) Warning: Frame 1457 Coordinates out of bounds (-1) Warning: Frame 1459 Coordinates out of bounds (-1) Warning: Frame 1460 Coordinates out of bounds (-1) Warning: Frame 1466 Coordinates out of bounds (-1) Warning: Frame 1479 Coordinates out of bounds (-1) Warning: Frame 1485 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 1514 Coordinates out of bounds (-1) Warning: Frame 1523 Coordinates out of bounds (-1) Warning: Frame 1524 Coordinates out of bounds (-1) Warning: Frame 1540 Coordinates out of bounds (-1) Warning: Frame 1541 Coordinates out of bounds (-1) Warning: Frame 1542 Coordinates out of bounds (-1) Warning: Frame 1545 Coordinates out of bounds (-1) Warning: Frame 1554 Coordinates out of bounds (-1) Warning: Frame 1557 Coordinates out of bounds (-1) Warning: Frame 1570 Coordinates out of bounds (-1) Warning: Frame 1572 Coordinates out of bounds (-1) Warning: Frame 1576 Coordinates out of bounds (-1) Warning: Frame 1614 Coordinates out of bounds (-1) Warning: Frame 1615 Coordinates out of bounds (-1) Warning: Frame 1619 Coordinates out of bounds (-1) Warning: Frame 1624 Coordinates out of bounds (-1) Warning: Frame 1625 Coordinates out of bounds (-1) Warning: Frame 1627 Coordinates out of bounds (-1) Warning: Frame 1628 Coordinates out of bounds (-1) Warning: Frame 1629 Coordinates out of bounds (-1) Warning: Frame 1632 Coordinates out of bounds (-1) Warning: Frame 1663 Coordinates out of bounds (-1) Warning: Frame 1672 Coordinates out of bounds (-1) Warning: Frame 1693 Coordinates out of bounds (-1) Warning: Frame 1708 Coordinates out of bounds (-1) Warning: Frame 1713 Coordinates out of bounds (-1) Warning: Frame 1714 Coordinates out of bounds (-1) Warning: Frame 1716 Coordinates out of bounds (-1) Warning: Frame 1734 Coordinates out of bounds (-1) Warning: Frame 1735 Coordinates out of bounds (-1) Warning: Frame 1739 Coordinates out of bounds (-1) Warning: Frame 1776 Coordinates out of bounds (-1) Warning: Frame 1777 Coordinates out of bounds (-1) Warning: Frame 1778 Coordinates out of bounds (-1) Warning: 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Warning: Frame 5079 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 4490 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 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: 5081 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 5081 TIME: Analyses took 0.0022 seconds. DATASETS (36 total): rms_2_aform "rms_2_aform" (double, rms), size is 5081 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 5081 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 5081 COM "COM" (double, distance), size is 5081 g1 "g1" (double, torsion(gamma)), size is 5081 d1 "d1" (double, torsion(delta)), size is 5081 e1 "e1" (double, torsion(epsilon)), size is 5081 z1 "z1" (double, torsion(zeta)), size is 5081 c1 "c1" (double, torsion(chin)), size is 5081 a2 "a2" (double, torsion(alpha)), size is 5081 b2 "b2" (double, torsion(beta)), size is 5081 g2 "g2" (double, torsion(gamma)), size is 5081 d2 "d2" (double, torsion(delta)), size is 5081 c2 "c2" (double, torsion(chin)), size is 5081 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 ( 0.05%) TIME: Trajectory Process : 0.0109 s ( 19.57%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0022 s ( 3.93%) TIME: Data File Write : 0.0427 s ( 76.40%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0558 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.1161 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.