CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:34:32 | Available memory: 1.485 GB INPUT: Reading input from 'pt-analysis1.in' [parm ../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c2] Reading '../ctraj.c2' as Amber NetCDF [reference ../../../B-form.pdb [a-form]] Reading '../../../B-form.pdb' as PDB Warning: PDB line length is short (67 chars, expected 80). Setting active reference for distance-based masks: 'B-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 COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7, 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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5465 of 5465) Coordinate processing will occur on 5465 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' (12 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 COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7 (11 atoms), imaged. 2: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 3: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 4: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 5: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 6: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 7: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 8: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 9: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 10: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 11: [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.c2 (1-5465, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5465 frames and processed 5465 frames. TIME: Avg. throughput= 114139.5155 frames / second. ACTION OUTPUT: DATASETS (12 total): rms_2_aform "rms_2_aform" (double, rms), size is 5465 COM "COM" (double, distance), size is 5465 g1 "g1" (double, torsion(gamma)), size is 5465 d1 "d1" (double, torsion(delta)), size is 5465 e1 "e1" (double, torsion(epsilon)), size is 5465 z1 "z1" (double, torsion(zeta)), size is 5465 c1 "c1" (double, torsion(chin)), size is 5465 a2 "a2" (double, torsion(alpha)), size is 5465 b2 "b2" (double, torsion(beta)), size is 5465 g2 "g2" (double, torsion(gamma)), size is 5465 d2 "d2" (double, torsion(delta)), size is 5465 c2 "c2" (double, torsion(chin)), size is 5465 RUN TIMING: TIME: Init : 0.0001 s ( 0.10%) TIME: Trajectory Process : 0.0479 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 ( 0.07%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0480 s ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Data set base name 'AVERAGE_00014' 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 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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5465 of 5465) Coordinate processing will occur on 5465 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c2 (1-5465, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5465 frames and processed 5465 frames. TIME: Avg. throughput= 463607.0580 frames / second. ACTION OUTPUT: ANALYSIS: Performing 13 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: 5465 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 5465 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: 5465 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 41 Coordinates out of bounds (-1) Warning: Frame 44 Coordinates out of bounds (-1) Warning: Frame 45 Coordinates out of bounds (-1) Warning: Frame 52 Coordinates out of bounds (-1) Warning: Frame 66 Coordinates out of bounds (-1) Warning: Frame 84 Coordinates out of bounds (-1) Warning: Frame 85 Coordinates out of bounds (-1) Warning: Frame 86 Coordinates out of bounds (-1) Warning: Frame 117 Coordinates out of bounds (-1) Warning: Frame 118 Coordinates out of bounds (-1) Warning: Frame 119 Coordinates out of bounds (-1) Warning: Frame 120 Coordinates out of bounds (-1) Warning: Frame 121 Coordinates out of bounds (-1) Warning: Frame 122 Coordinates out of bounds (-1) Warning: Frame 141 Coordinates out of bounds (-1) Warning: Frame 142 Coordinates out of bounds (-1) Warning: Frame 162 Coordinates out of bounds (-1) Warning: Frame 174 Coordinates out of bounds (-1) Warning: Frame 180 Coordinates out of bounds (-1) Warning: Frame 182 Coordinates out of bounds (-1) Warning: Frame 184 Coordinates out of bounds (-1) Warning: Frame 188 Coordinates out of bounds (-1) Warning: Frame 189 Coordinates out of bounds (-1) Warning: Frame 209 Coordinates out of bounds (-1) Warning: Frame 228 Coordinates out of bounds (-1) Warning: Frame 229 Coordinates out of bounds (-1) Warning: Frame 231 Coordinates out of bounds (-1) Warning: Frame 277 Coordinates out of bounds (-1) Warning: Frame 279 Coordinates out of bounds (-1) Warning: Frame 289 Coordinates out of bounds (-1) Warning: Frame 293 Coordinates out of bounds (-1) Warning: Frame 294 Coordinates out of bounds (-1) Warning: Frame 304 Coordinates out of bounds (-1) Warning: Frame 309 Coordinates out of bounds (-1) Warning: Frame 322 Coordinates out of bounds (-1) Warning: Frame 323 Coordinates out of bounds (-1) Warning: Frame 342 Coordinates out of bounds (-1) Warning: Frame 343 Coordinates out of bounds (-1) Warning: Frame 353 Coordinates out of bounds (-1) Warning: Frame 369 Coordinates out of bounds (-1) Warning: Frame 370 Coordinates out of bounds (-1) Warning: Frame 377 Coordinates out of bounds (-1) Warning: Frame 400 Coordinates out of bounds (-1) Warning: Frame 407 Coordinates out of bounds (-1) Warning: Frame 409 Coordinates out of bounds (-1) Warning: Frame 410 Coordinates out of bounds (-1) Warning: Frame 421 Coordinates out of bounds (-1) Warning: Frame 456 Coordinates out of bounds (-1) Warning: Frame 473 Coordinates out of bounds (-1) Warning: Frame 474 Coordinates out of bounds (-1) Warning: Frame 477 Coordinates out of bounds (-1) Warning: Frame 478 Coordinates out of bounds (-1) Warning: Frame 480 Coordinates out of bounds (-1) Warning: Frame 481 Coordinates out of bounds (-1) Warning: Frame 482 Coordinates out of bounds (-1) Warning: Frame 483 Coordinates out of bounds (-1) Warning: Frame 485 Coordinates out of bounds (-1) Warning: Frame 487 Coordinates out of bounds (-1) Warning: Frame 488 Coordinates out of bounds (-1) Warning: Frame 489 Coordinates out of bounds (-1) Warning: Frame 490 Coordinates out of bounds (-1) Warning: Frame 491 Coordinates out of bounds (-1) Warning: Frame 499 Coordinates out of bounds (-1) Warning: Frame 508 Coordinates out of bounds (-1) Warning: Frame 521 Coordinates out of bounds (-1) Warning: Frame 536 Coordinates out of bounds (-1) Warning: Frame 569 Coordinates out of bounds (-1) Warning: Frame 570 Coordinates out of bounds (-1) Warning: Frame 603 Coordinates out of bounds (-1) Warning: Frame 619 Coordinates out of bounds (-1) Warning: Frame 620 Coordinates out of bounds (-1) Warning: Frame 622 Coordinates out of bounds (-1) Warning: Frame 624 Coordinates out of bounds (-1) Warning: Frame 630 Coordinates out of bounds (-1) Warning: Frame 631 Coordinates out of bounds (-1) Warning: Frame 653 Coordinates out of bounds (-1) Warning: Frame 664 Coordinates out of bounds (-1) Warning: Frame 665 Coordinates out of bounds (-1) Warning: Frame 666 Coordinates out of bounds (-1) Warning: Frame 667 Coordinates out of bounds (-1) Warning: Frame 668 Coordinates out of bounds (-1) Warning: Frame 687 Coordinates out of bounds (-1) Warning: Frame 688 Coordinates out of bounds (-1) Warning: Frame 689 Coordinates out of bounds (-1) Warning: Frame 690 Coordinates out of bounds (-1) Warning: Frame 691 Coordinates out of bounds (-1) Warning: Frame 712 Coordinates out of bounds (-1) Warning: Frame 718 Coordinates out of bounds (-1) Warning: Frame 719 Coordinates out of bounds (-1) Warning: Frame 720 Coordinates out of bounds (-1) Warning: Frame 721 Coordinates out of bounds (-1) Warning: Frame 722 Coordinates out of bounds (-1) Warning: Frame 724 Coordinates out of bounds (-1) Warning: Frame 725 Coordinates out of bounds (-1) Warning: Frame 727 Coordinates out of bounds (-1) Warning: Frame 739 Coordinates out of bounds (-1) Warning: Frame 753 Coordinates out of bounds (-1) Warning: Frame 762 Coordinates out of bounds (-1) Warning: Frame 764 Coordinates out of bounds (-1) Warning: Frame 765 Coordinates out of bounds (-1) Warning: Frame 767 Coordinates out of bounds (-1) Warning: Frame 771 Coordinates out of bounds (-1) Warning: Frame 779 Coordinates out of bounds (-1) Warning: Frame 780 Coordinates out of bounds (-1) Warning: Frame 794 Coordinates out of bounds (-1) Warning: Frame 803 Coordinates out of bounds (-1) Warning: Frame 804 Coordinates out of bounds (-1) Warning: Frame 847 Coordinates out of bounds (-1) Warning: Frame 867 Coordinates out of bounds (-1) Warning: Frame 868 Coordinates out of bounds (-1) Warning: Frame 869 Coordinates out of bounds (-1) Warning: Frame 870 Coordinates out of bounds (-1) Warning: Frame 872 Coordinates out of bounds (-1) Warning: Frame 873 Coordinates out of bounds (-1) Warning: Frame 875 Coordinates out of bounds (-1) Warning: Frame 901 Coordinates out of bounds (-1) Warning: Frame 902 Coordinates out of bounds (-1) Warning: Frame 903 Coordinates out of bounds (-1) Warning: Frame 905 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 920 Coordinates out of bounds (-1) Warning: Frame 921 Coordinates out of bounds (-1) Warning: Frame 922 Coordinates out of bounds (-1) Warning: Frame 925 Coordinates out of bounds (-1) Warning: Frame 929 Coordinates out of bounds (-1) Warning: Frame 958 Coordinates out of bounds (-1) Warning: Frame 959 Coordinates out of bounds (-1) Warning: Frame 961 Coordinates out of bounds (-1) Warning: Frame 973 Coordinates out of bounds (-1) Warning: Frame 975 Coordinates out of bounds (-1) Warning: Frame 976 Coordinates out of bounds (-1) Warning: Frame 990 Coordinates out of bounds (-1) Warning: Frame 991 Coordinates out of bounds (-1) Warning: Frame 992 Coordinates out of bounds (-1) Warning: Frame 993 Coordinates out of bounds (-1) Warning: Frame 1007 Coordinates out of bounds (-1) Warning: Frame 1008 Coordinates out of bounds (-1) Warning: Frame 1010 Coordinates out of bounds (-1) Warning: Frame 1011 Coordinates out of bounds (-1) Warning: Frame 1021 Coordinates out of bounds (-1) Warning: Frame 1024 Coordinates out of bounds (-1) Warning: Frame 1028 Coordinates out of bounds (-1) Warning: Frame 1051 Coordinates out of bounds (-1) Warning: Frame 1055 Coordinates out of bounds (-1) Warning: Frame 1062 Coordinates out of bounds (-1) Warning: Frame 1074 Coordinates out of bounds (-1) Warning: Frame 1075 Coordinates out of bounds (-1) Warning: Frame 1083 Coordinates out of bounds (-1) Warning: Frame 1084 Coordinates out of bounds (-1) Warning: Frame 1108 Coordinates out of bounds (-1) Warning: Frame 1110 Coordinates out of bounds (-1) Warning: Frame 1118 Coordinates out of bounds (-1) Warning: Frame 1120 Coordinates out of bounds (-1) Warning: Frame 1121 Coordinates out of bounds (-1) Warning: Frame 1136 Coordinates out of bounds (-1) Warning: Frame 1138 Coordinates out of bounds (-1) Warning: Frame 1141 Coordinates out of bounds (-1) Warning: Frame 1142 Coordinates out of bounds (-1) Warning: Frame 1143 Coordinates out of bounds (-1) Warning: Frame 1152 Coordinates out of bounds (-1) Warning: Frame 1153 Coordinates out of bounds (-1) Warning: Frame 1154 Coordinates out of bounds (-1) Warning: Frame 1155 Coordinates out of bounds (-1) Warning: Frame 1159 Coordinates out of bounds (-1) Warning: Frame 1182 Coordinates out of bounds (-1) Warning: Frame 1183 Coordinates out of bounds (-1) Warning: Frame 1196 Coordinates out of bounds (-1) Warning: Frame 1216 Coordinates out of bounds (-1) Warning: Frame 1240 Coordinates out of bounds (-1) Warning: Frame 1257 Coordinates out of bounds (-1) Warning: Frame 1263 Coordinates out of bounds (-1) Warning: Frame 1278 Coordinates out of bounds (-1) Warning: Frame 1297 Coordinates out of bounds (-1) Warning: Frame 1298 Coordinates out of bounds (-1) Warning: Frame 1300 Coordinates out of bounds (-1) Warning: Frame 1349 Coordinates out of bounds (-1) Warning: Frame 1369 Coordinates out of bounds (-1) Warning: Frame 1373 Coordinates out of bounds (-1) Warning: Frame 1382 Coordinates out of bounds (-1) Warning: Frame 1383 Coordinates out of bounds (-1) Warning: Frame 1384 Coordinates out of bounds (-1) Warning: Frame 1391 Coordinates out of bounds (-1) Warning: Frame 1393 Coordinates out of bounds (-1) Warning: Frame 1394 Coordinates out of bounds (-1) Warning: Frame 1401 Coordinates out of bounds (-1) Warning: Frame 1404 Coordinates out of bounds (-1) Warning: Frame 1405 Coordinates out of bounds (-1) Warning: Frame 1407 Coordinates out of bounds (-1) Warning: Frame 1408 Coordinates out of bounds (-1) Warning: Frame 1430 Coordinates out of bounds (-1) Warning: Frame 1432 Coordinates out of bounds (-1) Warning: Frame 1433 Coordinates out of bounds (-1) Warning: Frame 1456 Coordinates out of bounds (-1) Warning: Frame 1457 Coordinates out of bounds (-1) Warning: Frame 1462 Coordinates out of bounds (-1) Warning: Frame 1463 Coordinates out of bounds (-1) Warning: Frame 1464 Coordinates out of bounds (-1) Warning: Frame 1465 Coordinates out of bounds (-1) Warning: Frame 1466 Coordinates out of bounds (-1) Warning: Frame 1467 Coordinates out of bounds (-1) Warning: Frame 1476 Coordinates out of bounds (-1) Warning: Frame 1490 Coordinates out of bounds (-1) Warning: Frame 1496 Coordinates out of bounds (-1) Warning: Frame 1531 Coordinates out of bounds (-1) Warning: Frame 1536 Coordinates out of bounds (-1) Warning: Frame 1544 Coordinates out of bounds (-1) Warning: Frame 1546 Coordinates out of bounds (-1) Warning: Frame 1549 Coordinates out of bounds (-1) Warning: Frame 1552 Coordinates out of bounds (-1) Warning: Frame 1553 Coordinates out of bounds (-1) Warning: Frame 1564 Coordinates out of bounds (-1) Warning: Frame 1571 Coordinates out of bounds (-1) Warning: Frame 1578 Coordinates out of bounds (-1) Warning: Frame 1587 Coordinates out of bounds (-1) Warning: Frame 1588 Coordinates out of bounds (-1) Warning: Frame 1589 Coordinates out of bounds (-1) Warning: Frame 1608 Coordinates out of bounds (-1) Warning: Frame 1630 Coordinates out of bounds (-1) Warning: Frame 1639 Coordinates out of bounds (-1) Warning: Frame 1662 Coordinates out of bounds (-1) Warning: Frame 1672 Coordinates out of bounds (-1) Warning: Frame 1684 Coordinates out of bounds (-1) Warning: Frame 1700 Coordinates out of bounds (-1) Warning: Frame 1704 Coordinates out of bounds (-1) Warning: Frame 1706 Coordinates out of bounds (-1) Warning: Frame 1713 Coordinates out of bounds (-1) Warning: Frame 1714 Coordinates out of bounds (-1) Warning: Frame 1718 Coordinates out of bounds (-1) Warning: Frame 1722 Coordinates out of bounds (-1) Warning: Frame 1723 Coordinates out of bounds (-1) Warning: Frame 1724 Coordinates out of bounds (-1) Warning: Frame 1725 Coordinates out of bounds (-1) Warning: Frame 1729 Coordinates out of bounds (-1) Warning: Frame 1732 Coordinates out of bounds (-1) Warning: Frame 1734 Coordinates out of bounds (-1) Warning: Frame 1735 Coordinates out of bounds (-1) Warning: Frame 1736 Coordinates out of bounds (-1) Warning: Frame 1739 Coordinates out of bounds (-1) Warning: Frame 1740 Coordinates out of bounds (-1) Warning: Frame 1751 Coordinates out of bounds (-1) Warning: Frame 1765 Coordinates out of bounds (-1) Warning: Frame 1771 Coordinates out of bounds (-1) Warning: Frame 1772 Coordinates out of bounds (-1) Warning: Frame 1788 Coordinates out of bounds (-1) Warning: Frame 1789 Coordinates out of bounds (-1) Warning: Frame 1807 Coordinates out of bounds (-1) Warning: Frame 1811 Coordinates out of bounds (-1) Warning: Frame 1830 Coordinates out of bounds (-1) Warning: Frame 1844 Coordinates out of bounds (-1) Warning: Frame 1863 Coordinates out of bounds (-1) Warning: Frame 1872 Coordinates out of bounds (-1) Warning: Frame 1896 Coordinates out of bounds (-1) Warning: Frame 1897 Coordinates out of bounds (-1) Warning: Frame 1899 Coordinates out of bounds (-1) Warning: Frame 1902 Coordinates out of bounds (-1) Warning: Frame 1931 Coordinates out of bounds (-1) Warning: Frame 1932 Coordinates out of bounds (-1) Warning: Frame 1945 Coordinates out of bounds (-1) Warning: Frame 1946 Coordinates out of bounds (-1) Warning: Frame 1947 Coordinates out of bounds (-1) Warning: Frame 1951 Coordinates out of bounds (-1) Warning: Frame 1952 Coordinates out of bounds (-1) Warning: Frame 1958 Coordinates out of bounds (-1) Warning: Frame 1973 Coordinates out of bounds (-1) Warning: Frame 1974 Coordinates out of bounds (-1) Warning: Frame 1980 Coordinates out of bounds (-1) Warning: Frame 2008 Coordinates out of bounds (-1) Warning: Frame 2013 Coordinates out of bounds (-1) Warning: Frame 2016 Coordinates out of bounds (-1) Warning: Frame 2031 Coordinates out of bounds (-1) Warning: Frame 2042 Coordinates out of bounds (-1) Warning: Frame 2043 Coordinates out of bounds (-1) Warning: Frame 2049 Coordinates out of bounds (-1) Warning: Frame 2050 Coordinates out of bounds (-1) Warning: Frame 2060 Coordinates out of bounds (-1) Warning: Frame 2095 Coordinates out of bounds (-1) Warning: Frame 2096 Coordinates out of bounds (-1) Warning: Frame 2102 Coordinates out of bounds (-1) Warning: Frame 2103 Coordinates out of bounds (-1) Warning: Frame 2104 Coordinates out of bounds (-1) Warning: Frame 2107 Coordinates out of bounds (-1) Warning: Frame 2123 Coordinates out of bounds (-1) Warning: Frame 2124 Coordinates out of bounds (-1) Warning: Frame 2138 Coordinates out of bounds (-1) Warning: Frame 2139 Coordinates out of bounds (-1) Warning: Frame 2140 Coordinates out of bounds (-1) Warning: Frame 2143 Coordinates out of bounds (-1) Warning: Frame 2179 Coordinates out of bounds (-1) Warning: Frame 2180 Coordinates out of bounds (-1) Warning: Frame 2215 Coordinates out of bounds (-1) Warning: Frame 2231 Coordinates out of bounds (-1) Warning: Frame 2240 Coordinates out of bounds (-1) Warning: Frame 2242 Coordinates out of bounds (-1) Warning: Frame 2243 Coordinates out of bounds (-1) Warning: Frame 2244 Coordinates out of bounds (-1) Warning: Frame 2246 Coordinates out of bounds (-1) Warning: Frame 2248 Coordinates out of bounds (-1) Warning: Frame 2249 Coordinates out of bounds (-1) Warning: Frame 2251 Coordinates out of bounds (-1) Warning: Frame 2252 Coordinates out of bounds (-1) Warning: Frame 2269 Coordinates out of bounds (-1) Warning: Frame 2282 Coordinates out of bounds (-1) Warning: Frame 2313 Coordinates out of bounds (-1) Warning: Frame 2326 Coordinates out of bounds (-1) Warning: Frame 2328 Coordinates out of bounds (-1) Warning: Frame 2337 Coordinates out of bounds (-1) Warning: Frame 2363 Coordinates out of bounds (-1) Warning: Frame 2364 Coordinates out of bounds (-1) Warning: Frame 2371 Coordinates out of bounds (-1) Warning: Frame 2373 Coordinates out of bounds (-1) Warning: Frame 2409 Coordinates out of bounds (-1) Warning: Frame 2423 Coordinates out of bounds (-1) Warning: Frame 2448 Coordinates out of bounds (-1) Warning: Frame 2449 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Warning: Frame 5384 Coordinates out of bounds (-1) Warning: Frame 5405 Coordinates out of bounds (-1) Warning: Frame 5412 Coordinates out of bounds (-1) Warning: Frame 5413 Coordinates out of bounds (-1) Warning: Frame 5416 Coordinates out of bounds (-1) Warning: Frame 5417 Coordinates out of bounds (-1) Warning: Frame 5419 Coordinates out of bounds (-1) Warning: Frame 5420 Coordinates out of bounds (-1) Warning: Frame 5421 Coordinates out of bounds (-1) Warning: Frame 5461 Coordinates out of bounds (-1) Warning: Frame 5464 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 4727 3: [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: 5465 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 5465 4: [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: 5465 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 5465 5: [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: 5465 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 5465 6: [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: 5465 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 5465 7: [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: 5465 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 5465 8: [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: 5465 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 5465 9: [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: 5465 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 5465 10: [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: 5465 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 5465 11: [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: 5465 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 5465 12: [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: 5465 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 5465 TIME: Analyses took 0.0020 seconds. DATASETS (31 total): rms_2_aform "rms_2_aform" (double, rms), size is 5465 COM "COM" (double, distance), size is 5465 g1 "g1" (double, torsion(gamma)), size is 5465 d1 "d1" (double, torsion(delta)), size is 5465 e1 "e1" (double, torsion(epsilon)), size is 5465 z1 "z1" (double, torsion(zeta)), size is 5465 c1 "c1" (double, torsion(chin)), size is 5465 a2 "a2" (double, torsion(alpha)), size is 5465 b2 "b2" (double, torsion(beta)), size is 5465 g2 "g2" (double, torsion(gamma)), size is 5465 d2 "d2" (double, torsion(delta)), size is 5465 c2 "c2" (double, torsion(chin)), size is 5465 AVERAGE_00014[avg] "AVERAGE_00014[avg]" (double), size is 1 AVERAGE_00014[sd] "AVERAGE_00014[sd]" (double), size is 1 AVERAGE_00014[ymin] "AVERAGE_00014[ymin]" (double), size is 1 AVERAGE_00014[ymax] "AVERAGE_00014[ymax]" (double), size is 1 AVERAGE_00014[yminidx] "AVERAGE_00014[yminidx]" (integer), size is 1 AVERAGE_00014[ymaxidx] "AVERAGE_00014[ymaxidx]" (integer), size is 1 AVERAGE_00014[names] "AVERAGE_00014[names]" (string), size is 1 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 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 (13 total): avg-rmsd-all.dat (Standard Data File): AVERAGE_00014[avg] AVERAGE_00014[sd] AVERAGE_00014[ymin] AVERAGE_00014[ymax] AVERAGE_00014[yminidx] AVERAGE_00014[ymaxidx] AVERAGE_00014[names] rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM 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 ( 0.09%) TIME: Trajectory Process : 0.0118 s ( 40.56%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0020 s ( 6.74%) TIME: Data File Write : 0.0153 s ( 52.54%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0291 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0906 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.