CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:03:02 | Available memory: 1.737 GB Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology INPUT: Reading input from 'pt-tors.in' [trajin ../ctraj.c3] Reading '../ctraj.c3' 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, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5593 of 5593) Coordinate processing will occur on 5593 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.c3 (1-5593, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5593 frames and processed 5593 frames. TIME: Avg. throughput= 254829.5972 frames / second. ACTION OUTPUT: DATASETS (7 total): d1 "d1" (double, torsion), size is 5593 e1 "e1" (double, torsion), size is 5593 z1 "z1" (double, torsion), size is 5593 a2 "a2" (double, torsion), size is 5593 b2 "b2" (double, torsion), size is 5593 g2 "g2" (double, torsion), size is 5593 d2' "d2'" (double, torsion), size is 5593 DATAFILES (1 total): tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2' RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.0219 s ( 25.58%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0638 s ( 74.35%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0858 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0965 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.