CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/23/15 18:08:13
| Available memory: 52621.4 MB
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
INPUT: Reading Input from file 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:
0: 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 39854 frames
INPUT TRAJECTORIES:
0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 39854 of 39854)
Coordinate processing will occur on 39854 frames.
TIME: Run Initialization took 0.0000 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.c5 (1-39854, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 39854 frames and processed 39854 frames.
TIME: Trajectory processing: 0.0649 s
TIME: Avg. throughput= 614490.3403 frames / second.
ACTION OUTPUT:
DATASETS:
7 data sets:
d1 "d1" (double, torsion), size is 39854
e1 "e1" (double, torsion), size is 39854
z1 "z1" (double, torsion), size is 39854
a2 "a2" (double, torsion), size is 39854
b2 "b2" (double, torsion), size is 39854
g2 "g2" (double, torsion), size is 39854
d2' "d2'" (double, torsion), size is 39854
DATAFILES:
tors1.dat (Standard Data File): d1 e1 z1 a2 b2 g2 d2'
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.2671 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.