CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 13:04:25 | Available memory: 6.550 GB Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology INPUT: Reading input from 'pt-tors.in' [trajin ../ctraj.c4] Reading '../ctraj.c4' 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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6306 of 6306) Coordinate processing will occur on 6306 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.c4 (1-6306, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 6306 frames and processed 6306 frames. TIME: Avg. throughput= 51901.2346 frames / second. ACTION OUTPUT: DATASETS (7 total): d1 "d1" (double, torsion), size is 6306 e1 "e1" (double, torsion), size is 6306 z1 "z1" (double, torsion), size is 6306 a2 "a2" (double, torsion), size is 6306 b2 "b2" (double, torsion), size is 6306 g2 "g2" (double, torsion), size is 6306 d2' "d2'" (double, torsion), size is 6306 DATAFILES (1 total): tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2' RUN TIMING: TIME: Init : 0.0002 s ( 0.04%) TIME: Trajectory Process : 0.1215 s ( 34.35%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.2319 s ( 65.55%) TIME: Other : 0.0002 s ( 0.00%) TIME: Run Total 0.3537 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.3994 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.