CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 12/03/15 15:34:40
| Available memory: 53217.3 MB
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
INPUT: Reading Input from file pt-tors.in
[trajin ../ctraj.c1]
Reading '../ctraj.c1' 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:
0: 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 140560 frames
INPUT TRAJECTORIES:
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 140560 of 140560)
Coordinate processing will occur on 140560 frames.
TIME: Run Initialization took 0.0004 seconds.
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.c1 (1-140560, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 140560 frames and processed 140560 frames.
TIME: Trajectory processing: 0.2316 s
TIME: Avg. throughput= 606777.4660 frames / second.
ACTION OUTPUT:
DATASETS:
7 data sets:
d1 "d1" (double, torsion), size is 140560
e1 "e1" (double, torsion), size is 140560
z1 "z1" (double, torsion), size is 140560
a2 "a2" (double, torsion), size is 140560
b2 "b2" (double, torsion), size is 140560
g2 "g2" (double, torsion), size is 140560
d2' "d2'" (double, torsion), size is 140560
DATAFILES:
tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2'
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.8702 seconds.
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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.