CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 15:01:36 | Available memory: 1.472 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.c1] Reading '../ctraj.c1' 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12345 of 12345) Coordinate processing will occur on 12345 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.c1 (1-12345, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 12345 frames and processed 12345 frames. TIME: Avg. throughput= 114839.3458 frames / second. ACTION OUTPUT: DATASETS (12 total): rms_2_aform "rms_2_aform" (double, rms), size is 12345 COM "COM" (double, distance), size is 12345 g1 "g1" (double, torsion(gamma)), size is 12345 d1 "d1" (double, torsion(delta)), size is 12345 e1 "e1" (double, torsion(epsilon)), size is 12345 z1 "z1" (double, torsion(zeta)), size is 12345 c1 "c1" (double, torsion(chin)), size is 12345 a2 "a2" (double, torsion(alpha)), size is 12345 b2 "b2" (double, torsion(beta)), size is 12345 g2 "g2" (double, torsion(gamma)), size is 12345 d2 "d2" (double, torsion(delta)), size is 12345 c2 "c2" (double, torsion(chin)), size is 12345 RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1075 s ( 99.91%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.03%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1076 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12345 of 12345) Coordinate processing will occur on 12345 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c1 (1-12345, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 12345 frames and processed 12345 frames. TIME: Avg. throughput= 502462.4527 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: 12345 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 12345 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: 12345 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 211 Coordinates out of bounds (-1) Warning: Frame 269 Coordinates out of bounds (-1) Warning: Frame 270 Coordinates out of bounds (-1) Warning: Frame 300 Coordinates out of bounds (-1) Warning: Frame 359 Coordinates out of bounds (-1) Warning: Frame 398 Coordinates out of bounds (-1) Warning: Frame 408 Coordinates out of bounds (-1) Warning: Frame 465 Coordinates out of bounds (-1) Warning: Frame 630 Coordinates out of bounds (-1) Warning: Frame 631 Coordinates out of bounds (-1) Warning: Frame 711 Coordinates out of bounds (-1) Warning: Frame 800 Coordinates out of bounds (-1) Warning: Frame 857 Coordinates out of bounds (-1) Warning: Frame 868 Coordinates out of bounds (-1) Warning: Frame 1068 Coordinates out of bounds (-1) Warning: Frame 1083 Coordinates out of bounds (-1) Warning: Frame 1127 Coordinates out of bounds (-1) Warning: Frame 1282 Coordinates out of bounds (-1) Warning: Frame 1316 Coordinates out of bounds (-1) Warning: Frame 1344 Coordinates out of bounds (-1) Warning: Frame 1383 Coordinates out of bounds (-1) Warning: Frame 1398 Coordinates out of bounds (-1) Warning: Frame 1507 Coordinates out of bounds (-1) Warning: Frame 1672 Coordinates out of bounds (-1) Warning: Frame 1691 Coordinates out of bounds (-1) Warning: Frame 1692 Coordinates out of bounds (-1) Warning: Frame 1767 Coordinates out of bounds (-1) Warning: Frame 1948 Coordinates out of bounds (-1) Warning: Frame 2271 Coordinates out of bounds (-1) Warning: Frame 2281 Coordinates out of bounds (-1) Warning: Frame 2393 Coordinates out of bounds (-1) Warning: Frame 2449 Coordinates out of bounds (-1) Warning: Frame 2522 Coordinates out of bounds (-1) Warning: Frame 2620 Coordinates out of bounds (-1) Warning: Frame 2754 Coordinates out of bounds (-1) Warning: Frame 2779 Coordinates out of bounds (-1) Warning: Frame 2852 Coordinates out of bounds (-1) Warning: Frame 2940 Coordinates out of bounds (-1) Warning: Frame 2990 Coordinates out of bounds (-1) Warning: Frame 2991 Coordinates out of bounds (-1) Warning: Frame 3013 Coordinates out of bounds (-1) Warning: Frame 3073 Coordinates out of bounds (-1) Warning: Frame 3151 Coordinates out of bounds (-1) Warning: Frame 3200 Coordinates out of bounds (-1) Warning: Frame 3248 Coordinates out of bounds (-1) Warning: Frame 3271 Coordinates out of bounds (-1) Warning: Frame 3374 Coordinates out of bounds (-1) Warning: Frame 3423 Coordinates out of bounds (-1) Warning: Frame 3498 Coordinates out of bounds (-1) Warning: Frame 3709 Coordinates out of bounds (-1) Warning: Frame 3794 Coordinates out of bounds (-1) Warning: Frame 4014 Coordinates out of bounds (-1) Warning: Frame 4069 Coordinates out of bounds (-1) Warning: Frame 4180 Coordinates out of bounds (-1) Warning: Frame 4376 Coordinates out of bounds (-1) Warning: Frame 4377 Coordinates out of bounds (-1) Warning: Frame 4402 Coordinates out of bounds (-1) Warning: Frame 4420 Coordinates out of bounds (-1) Warning: Frame 4546 Coordinates out of bounds (-1) Warning: Frame 4560 Coordinates out of bounds (-1) Warning: Frame 4563 Coordinates out of bounds (-1) Warning: Frame 4626 Coordinates out of bounds (-1) Warning: Frame 4754 Coordinates out of bounds (-1) Warning: Frame 5101 Coordinates out of bounds (-1) Warning: Frame 5136 Coordinates out of bounds (-1) Warning: Frame 5151 Coordinates out of bounds (-1) Warning: Frame 5164 Coordinates out of bounds (-1) Warning: Frame 5235 Coordinates out of bounds (-1) Warning: Frame 5251 Coordinates out of bounds (-1) Warning: Frame 5253 Coordinates out of bounds (-1) Warning: Frame 5348 Coordinates out of bounds (-1) Warning: Frame 5380 Coordinates out of bounds (-1) Warning: Frame 5608 Coordinates out of bounds (-1) Warning: Frame 5629 Coordinates out of bounds (-1) Warning: Frame 5632 Coordinates out of bounds (-1) Warning: Frame 5633 Coordinates out of bounds (-1) Warning: Frame 5693 Coordinates out of bounds (-1) Warning: Frame 5959 Coordinates out of bounds (-1) Warning: Frame 6023 Coordinates out of bounds (-1) Warning: Frame 6037 Coordinates out of bounds (-1) Warning: Frame 6213 Coordinates out of bounds (-1) Warning: Frame 6228 Coordinates out of bounds (-1) Warning: Frame 6401 Coordinates out of bounds (-1) Warning: Frame 6402 Coordinates out of bounds (-1) Warning: Frame 6548 Coordinates out of bounds (-1) Warning: Frame 6552 Coordinates out of bounds (-1) Warning: Frame 6558 Coordinates out of bounds (-1) Warning: Frame 6725 Coordinates out of bounds (-1) Warning: Frame 6867 Coordinates out of bounds (-1) Warning: Frame 6868 Coordinates out of bounds (-1) Warning: Frame 6950 Coordinates out of bounds (-1) Warning: Frame 6964 Coordinates out of bounds (-1) Warning: Frame 6965 Coordinates out of bounds (-1) Warning: Frame 6966 Coordinates out of bounds (-1) Warning: Frame 7137 Coordinates out of bounds (-1) Warning: Frame 7138 Coordinates out of bounds (-1) Warning: Frame 7140 Coordinates out of bounds (-1) Warning: Frame 7250 Coordinates out of bounds (-1) Warning: Frame 7266 Coordinates out of bounds (-1) Warning: Frame 7267 Coordinates out of bounds (-1) Warning: Frame 7269 Coordinates out of bounds (-1) Warning: Frame 7271 Coordinates out of bounds (-1) Warning: Frame 7310 Coordinates out of bounds (-1) Warning: Frame 7415 Coordinates out of bounds (-1) Warning: Frame 7469 Coordinates out of bounds (-1) Warning: Frame 7713 Coordinates out of bounds (-1) Warning: Frame 7745 Coordinates out of bounds (-1) Warning: Frame 7802 Coordinates out of bounds (-1) Warning: Frame 8020 Coordinates out of bounds (-1) Warning: Frame 8079 Coordinates out of bounds (-1) Warning: Frame 8111 Coordinates out of bounds (-1) Warning: Frame 8293 Coordinates out of bounds (-1) Warning: Frame 8341 Coordinates out of bounds (-1) Warning: Frame 8342 Coordinates out of bounds (-1) Warning: Frame 8384 Coordinates out of bounds (-1) Warning: Frame 8431 Coordinates out of bounds (-1) Warning: Frame 8521 Coordinates out of bounds (-1) Warning: Frame 8578 Coordinates out of bounds (-1) Warning: Frame 8579 Coordinates out of bounds (-1) Warning: Frame 8580 Coordinates out of bounds (-1) Warning: Frame 8591 Coordinates out of bounds (-1) Warning: Frame 8602 Coordinates out of bounds (-1) Warning: Frame 8650 Coordinates out of bounds (-1) Warning: Frame 8669 Coordinates out of bounds (-1) Warning: Frame 8779 Coordinates out of bounds (-1) Warning: Frame 8881 Coordinates out of bounds (-1) Warning: Frame 9036 Coordinates out of bounds (-1) Warning: Frame 9055 Coordinates out of bounds (-1) Warning: Frame 9080 Coordinates out of bounds (-1) Warning: Frame 9100 Coordinates out of bounds (-1) Warning: Frame 9208 Coordinates out of bounds (-1) Warning: Frame 9424 Coordinates out of bounds (-1) Warning: Frame 9631 Coordinates out of bounds (-1) Warning: Frame 9640 Coordinates out of bounds (-1) Warning: Frame 9651 Coordinates out of bounds (-1) Warning: Frame 9758 Coordinates out of bounds (-1) Warning: Frame 9832 Coordinates out of bounds (-1) Warning: Frame 9851 Coordinates out of bounds (-1) Warning: Frame 9891 Coordinates out of bounds (-1) Warning: Frame 9961 Coordinates out of bounds (-1) Warning: Frame 10082 Coordinates out of bounds (-1) Warning: Frame 10086 Coordinates out of bounds (-1) Warning: Frame 10126 Coordinates out of bounds (-1) Warning: Frame 10127 Coordinates out of bounds (-1) Warning: Frame 10128 Coordinates out of bounds (-1) Warning: Frame 10283 Coordinates out of bounds (-1) Warning: Frame 10400 Coordinates out of bounds (-1) Warning: Frame 10539 Coordinates out of bounds (-1) Warning: Frame 10561 Coordinates out of bounds (-1) Warning: Frame 10728 Coordinates out of bounds (-1) Warning: Frame 10928 Coordinates out of bounds (-1) Warning: Frame 11034 Coordinates out of bounds (-1) Warning: Frame 11048 Coordinates out of bounds (-1) Warning: Frame 11249 Coordinates out of bounds (-1) Warning: Frame 11396 Coordinates out of bounds (-1) Warning: Frame 11462 Coordinates out of bounds (-1) Warning: Frame 11490 Coordinates out of bounds (-1) Warning: Frame 11559 Coordinates out of bounds (-1) Warning: Frame 11608 Coordinates out of bounds (-1) Warning: Frame 11776 Coordinates out of bounds (-1) Warning: Frame 11937 Coordinates out of bounds (-1) Warning: Frame 12099 Coordinates out of bounds (-1) Warning: Frame 12106 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 12182 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 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: 12345 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 12345 TIME: Analyses took 0.0034 seconds. DATASETS (31 total): rms_2_aform "rms_2_aform" (double, rms), size is 12345 COM "COM" (double, distance), size is 12345 g1 "g1" (double, torsion(gamma)), size is 12345 d1 "d1" (double, torsion(delta)), size is 12345 e1 "e1" (double, torsion(epsilon)), size is 12345 z1 "z1" (double, torsion(zeta)), size is 12345 c1 "c1" (double, torsion(chin)), size is 12345 a2 "a2" (double, torsion(alpha)), size is 12345 b2 "b2" (double, torsion(beta)), size is 12345 g2 "g2" (double, torsion(gamma)), size is 12345 d2 "d2" (double, torsion(delta)), size is 12345 c2 "c2" (double, torsion(chin)), size is 12345 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 ( 0.03%) TIME: Trajectory Process : 0.0246 s ( 27.70%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0034 s ( 3.78%) TIME: Data File Write : 0.0607 s ( 68.47%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0887 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.2116 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.