CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 05/26/16 11:30:22
| Available memory: 1.741 GB
INPUT: Reading input from 'pt-diheds.in'
[parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr]
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[strip :WAT,Na+,K+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../ctraj.c0]
Reading '../ctraj.c0' as Amber NetCDF
[dihedral c1c4 :1@H1' :1@C1' :1@N1 :1@C2 out diheds.dat]
DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N1]-[:1@C2]
Output range is -180 to 180 degrees.
[dihedral c1c8 :1@H1' :1@C1' :1@N1 :1@C6 out diheds.dat]
DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N1]-[:1@C6]
Output range is -180 to 180 degrees.
[dihedral c2c4 :2@H1' :2@C1' :2@N9 :2@C4 out diheds.dat]
DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N9]-[:2@C4]
Output range is -180 to 180 degrees.
[dihedral c2c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat]
DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N9]-[:2@C8]
Output range is -180 to 180 degrees.
[dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat]
DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P]
Output range is -180 to 180 degrees.
[dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat]
DIHEDRAL: [:1@C2']-[:1@C3']-[:1@O3']-[:2@P]
Output range is -180 to 180 degrees.
[dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat]
DIHEDRAL: [:1@H3']-[:1@C3']-[:1@O3']-[:2@P]
Output range is -180 to 180 degrees.
[dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat]
DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4']
Output range is -180 to 180 degrees.
[dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat]
DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5']
Output range is -180 to 180 degrees.
[dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat]
DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5']
Output range is -180 to 180 degrees.
[dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat]
DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5'']
Output range is -180 to 180 degrees.
[dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat]
DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5'']
Output range is -180 to 180 degrees.
[dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat]
DIHEDRAL: [:1@H3']-[:1@C3']-[:1@C4']-[:1@H4']
Output range is -180 to 180 degrees.
[dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat]
DIHEDRAL: [:2@H3']-[:2@C3']-[:2@C4']-[:2@H4']
Output range is -180 to 180 degrees.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 170542 of 170542)
Coordinate processing will occur on 170542 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (16 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr'
Warning: Setup incomplete for [strip]: Skipping
1: [autoimage origin]
Anchor molecule is 1
0 molecules are mobile.
2: [dihedral c1c4 :1@H1' :1@C1' :1@N1 :1@C2 out diheds.dat]
[:1@H1'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
3: [dihedral c1c8 :1@H1' :1@C1' :1@N1 :1@C6 out diheds.dat]
[:1@H1'](1) [:1@C1'](1) [:1@N1](1) [:1@C6](1)
4: [dihedral c2c4 :2@H1' :2@C1' :2@N9 :2@C4 out diheds.dat]
[:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
5: [dihedral c2c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat]
[:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C8](1)
6: [dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
7: [dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat]
[:1@C2'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
8: [dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat]
[:1@H3'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
9: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat]
[:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1)
10: [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat]
[:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5'](1)
11: [dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat]
[:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5'](1)
12: [dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat]
[:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5''](1)
13: [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat]
[:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5''](1)
14: [dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat]
[:1@H3'](1) [:1@C3'](1) [:1@C4'](1) [:1@H4'](1)
15: [dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat]
[:2@H3'](1) [:2@C3'](1) [:2@C4'](1) [:2@H4'](1)
----- ctraj.c0 (1-170542, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 170542 frames and processed 170542 frames.
TIME: Avg. throughput= 123097.9553 frames / second.
ACTION OUTPUT:
DATASETS (14 total):
c1c4 "c1c4" (double, torsion), size is 170542
c1c8 "c1c8" (double, torsion), size is 170542
c2c4 "c2c4" (double, torsion), size is 170542
c2c8 "c2c8" (double, torsion), size is 170542
e1c4 "e1c4" (double, torsion), size is 170542
e1c2 "e1c2" (double, torsion), size is 170542
e1h3 "e1h3" (double, torsion), size is 170542
b2 "b2" (double, torsion), size is 170542
g1h4ph5p "g1h4ph5p" (double, torsion), size is 170542
g2h4ph5p "g2h4ph5p" (double, torsion), size is 170542
g1h4ph5s "g1h4ph5s" (double, torsion), size is 170542
g2h4ph5s "g2h4ph5s" (double, torsion), size is 170542
d1h3ph4p "d1h3ph4p" (double, torsion), size is 170542
d2h3ph4p "d2h3ph4p" (double, torsion), size is 170542
DATAFILES (1 total):
diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5s g2h4ph5s d1h3ph4p d2h3ph4p
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 1.3854 s ( 38.40%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 2.2227 s ( 61.60%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 3.6082 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 3.7359 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.