CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 11:57:32 | Available memory: 1.738 GB Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology INPUT: Reading input from 'pt-tors.in' [trajin ../ctraj.c2] Reading '../ctraj.c2' as Amber NetCDF [dihedral d1 out tors1.dat :1@C5' :1@C4' :1@C3' :1@O3'] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 out tors1.dat :1@C4' :1@C3' :1@O3' :2@P] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 out tors1.dat :1@C3' :1@O3' :2@P :2@O5'] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral a2 out tors1.dat :1@O3' :2@P :2@O5' :2@C5'] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 out tors1.dat :2@P :2@O5' :2@C5' :2@C4'] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 out tors1.dat :2@O5' :2@C5' :2@C4' :2@C3'] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2' out tors1.dat :2@C5' :2@C4' :2@C3' :2@O3'] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 62 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 12463 of 12463) Coordinate processing will occur on 12463 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [dihedral d1 out tors1.dat :1@C5' :1@C4' :1@C3' :1@O3'] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral e1 out tors1.dat :1@C4' :1@C3' :1@O3' :2@P] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 2: [dihedral z1 out tors1.dat :1@C3' :1@O3' :2@P :2@O5'] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 3: [dihedral a2 out tors1.dat :1@O3' :2@P :2@O5' :2@C5'] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 4: [dihedral b2 out tors1.dat :2@P :2@O5' :2@C5' :2@C4'] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 5: [dihedral g2 out tors1.dat :2@O5' :2@C5' :2@C4' :2@C3'] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 6: [dihedral d2' out tors1.dat :2@C5' :2@C4' :2@C3' :2@O3'] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) ----- ctraj.c2 (1-12463, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 12463 frames and processed 12463 frames. TIME: Avg. throughput= 268338.8955 frames / second. ACTION OUTPUT: DATASETS (7 total): d1 "d1" (double, torsion), size is 12463 e1 "e1" (double, torsion), size is 12463 z1 "z1" (double, torsion), size is 12463 a2 "a2" (double, torsion), size is 12463 b2 "b2" (double, torsion), size is 12463 g2 "g2" (double, torsion), size is 12463 d2' "d2'" (double, torsion), size is 12463 DATAFILES (1 total): tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2' RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.0464 s ( 21.83%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.1663 s ( 78.14%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2128 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.2236 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.