CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:16:26 | Available memory: 1.723 GB Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology INPUT: Reading input from 'pt-tors.in' [trajin ../ctraj.c5] Reading '../ctraj.c5' 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, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3729 of 3729) Coordinate processing will occur on 3729 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.c5 (1-3729, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 3729 frames and processed 3729 frames. TIME: Avg. throughput= 13329.7587 frames / second. ACTION OUTPUT: DATASETS (7 total): d1 "d1" (double, torsion), size is 3729 e1 "e1" (double, torsion), size is 3729 z1 "z1" (double, torsion), size is 3729 a2 "a2" (double, torsion), size is 3729 b2 "b2" (double, torsion), size is 3729 g2 "g2" (double, torsion), size is 3729 d2' "d2'" (double, torsion), size is 3729 DATAFILES (1 total): tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2' RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.2797 s ( 29.77%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.6599 s ( 70.22%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.9398 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 4.1214 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.