CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:32:31 | Available memory: 1.205 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, 59 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 33875 of 33875) Coordinate processing will occur on 33875 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 (1-33875, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 33875 frames and processed 33875 frames. TIME: Avg. throughput= 263395.2523 frames / second. ACTION OUTPUT: DATASETS (7 total): d1 "d1" (double, torsion), size is 33875 e1 "e1" (double, torsion), size is 33875 z1 "z1" (double, torsion), size is 33875 a2 "a2" (double, torsion), size is 33875 b2 "b2" (double, torsion), size is 33875 g2 "g2" (double, torsion), size is 33875 d2' "d2'" (double, torsion), size is 33875 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 : 0.1286 s ( 25.16%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.3825 s ( 74.83%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5111 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.5222 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.