CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/22/16 13:05:03
| Available memory: 1.634 GB
INPUT: Reading input from 'pt-analysis.chi-py.in'
[parm ../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apa]]
Reading '../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apg]]
Reading '../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpa]]
Reading '../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpg]]
Reading '../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apc]]
Reading '../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apu]]
Reading '../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpc]]
Reading '../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpu]]
Reading '../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpa]]
Reading '../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpg]]
Reading '../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upa]]
Reading '../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upg]]
Reading '../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpc]]
Reading '../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpu]]
Reading '../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upc]]
Reading '../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[parm ../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upu]]
Reading '../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[trajin ../../ca/cluster-all/km-6/ctraj.c0 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c0' as Amber NetCDF
[trajin ../../ca/cluster-all/km-6/ctraj.c1 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c1' as Amber NetCDF
[trajin ../../ca/cluster-all/km-6/ctraj.c2 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c2' as Amber NetCDF
[trajin ../../ca/cluster-all/km-6/ctraj.c3 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c3' as Amber NetCDF
[trajin ../../ca/cluster-all/km-6/ctraj.c4 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c4' as Amber NetCDF
[trajin ../../ca/cluster-all/km-6/ctraj.c5 parm [cpa]]
Reading '../../ca/cluster-all/km-6/ctraj.c5' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c0 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c0' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c1 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c1' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c2 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c2' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c3 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c3' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c4 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c4' as Amber NetCDF
[trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c5 parm [cpg]]
Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c5' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c0 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c0' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c1 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c1' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c2 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c2' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c3 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c3' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c4 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c4' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c5 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c5' as Amber NetCDF
[trajin ../../ua/cluster-1-1/km-7/ctraj.c6 parm [upa]]
Reading '../../ua/cluster-1-1/km-7/ctraj.c6' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c0 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c0' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c1 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c1' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c2 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c2' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c3 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c3' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c4 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c4' as Amber NetCDF
[trajin ../../ug/cluster-1-1/km-6/ctraj.c5 parm [upg]]
Reading '../../ug/cluster-1-1/km-6/ctraj.c5' as Amber NetCDF
[trajin ../../cc/cluster-all/km-5/ctraj.c0 parm [cpc]]
Reading '../../cc/cluster-all/km-5/ctraj.c0' as Amber NetCDF
[trajin ../../cc/cluster-all/km-5/ctraj.c1 parm [cpc]]
Reading '../../cc/cluster-all/km-5/ctraj.c1' as Amber NetCDF
[trajin ../../cc/cluster-all/km-5/ctraj.c2 parm [cpc]]
Reading '../../cc/cluster-all/km-5/ctraj.c2' as Amber NetCDF
[trajin ../../cc/cluster-all/km-5/ctraj.c3 parm [cpc]]
Reading '../../cc/cluster-all/km-5/ctraj.c3' as Amber NetCDF
[trajin ../../cc/cluster-all/km-5/ctraj.c4 parm [cpc]]
Reading '../../cc/cluster-all/km-5/ctraj.c4' as Amber NetCDF
[trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c0 parm [cpu]]
Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c0' as Amber NetCDF
[trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c1 parm [cpu]]
Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c1' as Amber NetCDF
[trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c2 parm [cpu]]
Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c2' as Amber NetCDF
[trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c3 parm [cpu]]
Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c3' as Amber NetCDF
[trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c4 parm [cpu]]
Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c4' as Amber NetCDF
[trajin ../../uc/cluster-1-1/km-5/ctraj.c0 parm [upc]]
Reading '../../uc/cluster-1-1/km-5/ctraj.c0' as Amber NetCDF
[trajin ../../uc/cluster-1-1/km-5/ctraj.c1 parm [upc]]
Reading '../../uc/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF
[trajin ../../uc/cluster-1-1/km-5/ctraj.c2 parm [upc]]
Reading '../../uc/cluster-1-1/km-5/ctraj.c2' as Amber NetCDF
[trajin ../../uc/cluster-1-1/km-5/ctraj.c3 parm [upc]]
Reading '../../uc/cluster-1-1/km-5/ctraj.c3' as Amber NetCDF
[trajin ../../uc/cluster-1-1/km-5/ctraj.c4 parm [upc]]
Reading '../../uc/cluster-1-1/km-5/ctraj.c4' as Amber NetCDF
[trajin ../../uu/cluster-all/km-5/ctraj.c0 parm [upu]]
Reading '../../uu/cluster-all/km-5/ctraj.c0' as Amber NetCDF
[trajin ../../uu/cluster-all/km-5/ctraj.c1 parm [upu]]
Reading '../../uu/cluster-all/km-5/ctraj.c1' as Amber NetCDF
[trajin ../../uu/cluster-all/km-5/ctraj.c2 parm [upu]]
Reading '../../uu/cluster-all/km-5/ctraj.c2' as Amber NetCDF
[trajin ../../uu/cluster-all/km-5/ctraj.c3 parm [upu]]
Reading '../../uu/cluster-all/km-5/ctraj.c3' as Amber NetCDF
[trajin ../../uu/cluster-all/km-5/ctraj.c4 parm [upu]]
Reading '../../uu/cluster-all/km-5/ctraj.c4' as Amber NetCDF
[distance dist3 :1@HO5' :1@O2]
DISTANCE: :1@HO5' to :1@O2, center of mass.
[dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2]
Output range is -180 to 180 degrees.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (16 total):
0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (45 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 172040 of 172040)
1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142)
2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741)
3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630)
4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 74884 of 74884)
5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41559 of 41559)
6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201)
7: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 21662 of 21662)
8: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719)
9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023)
10: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4545 of 4545)
11: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3850 of 3850)
12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866)
13: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590)
14: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 13501 of 13501)
15: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487)
16: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4720 of 4720)
17: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3875 of 3875)
18: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1961 of 1961)
19: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458)
20: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072)
21: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18784 of 18784)
22: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656)
23: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3855 of 3855)
24: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3175 of 3175)
25: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041)
26: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387)
27: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 76671 of 76671)
28: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544)
29: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 48280 of 48280)
30: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868)
31: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571)
32: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10292 of 10292)
33: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7787 of 7787)
34: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482)
35: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137)
36: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062)
37: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 15117 of 15117)
38: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047)
39: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10637 of 10637)
40: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909)
41: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351)
42: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296)
43: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 86746 of 86746)
44: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 68322 of 68322)
Coordinate processing will occur on 2297543 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-172040, 1) -----
0%
----- ctraj.c1 (1-145142, 1) -----
10%
----- ctraj.c2 (1-88741, 1) -----
----- ctraj.c3 (1-77630, 1) -----
20%
----- ctraj.c4 (1-74884, 1) -----
----- ctraj.c5 (1-41559, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-40201, 1) -----
----- ctraj.c1 (1-21662, 1) -----
----- ctraj.c2 (1-17719, 1) -----
----- ctraj.c3 (1-12023, 1) -----
30%
----- ctraj.c4 (1-4545, 1) -----
----- ctraj.c5 (1-3850, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-50866, 1) -----
----- ctraj.c1 (1-18590, 1) -----
----- ctraj.c2 (1-13501, 1) -----
----- ctraj.c3 (1-6487, 1) -----
----- ctraj.c4 (1-4720, 1) -----
----- ctraj.c5 (1-3875, 1) -----
----- ctraj.c6 (1-1961, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-49458, 1) -----
----- ctraj.c1 (1-19072, 1) -----
----- ctraj.c2 (1-18784, 1) -----
----- ctraj.c3 (1-5656, 1) -----
----- ctraj.c4 (1-3855, 1) -----
----- ctraj.c5 (1-3175, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-273041, 1) -----
40% 50%
----- ctraj.c1 (1-134387, 1) -----
----- ctraj.c2 (1-76671, 1) -----
60%
----- ctraj.c3 (1-67544, 1) -----
----- ctraj.c4 (1-48280, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-55868, 1) -----
----- ctraj.c1 (1-18571, 1) -----
----- ctraj.c2 (1-10292, 1) -----
----- ctraj.c3 (1-7787, 1) -----
----- ctraj.c4 (1-7482, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-36137, 1) -----
70%
----- ctraj.c1 (1-27062, 1) -----
----- ctraj.c2 (1-15117, 1) -----
----- ctraj.c3 (1-11047, 1) -----
----- ctraj.c4 (1-10637, 1) -----
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions):
0: [distance dist3 :1@HO5' :1@O2]
:1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged.
1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
----- ctraj.c0 (1-225909, 1) -----
80%
----- ctraj.c1 (1-126351, 1) -----
----- ctraj.c2 (1-90296, 1) -----
90%
----- ctraj.c3 (1-86746, 1) -----
----- ctraj.c4 (1-68322, 1) -----
100% Complete.
Read 2297543 frames and processed 2297543 frames.
TIME: Avg. throughput= 681686.0280 frames / second.
ACTION OUTPUT:
DATASETS (2 total):
dist3 "dist3" (double, distance), size is 2297543
c1 "c1" (double, torsion(chin)), size is 2297543
RUN TIMING:
TIME: Init : 0.0005 s ( 0.01%)
TIME: Trajectory Process : 3.3704 s ( 99.98%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 3.3709 s
---------- RUN END ---------------------------------------------------
[hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-py.gnu norm]
Hist: 2dhist_c1_dist3-py.gnu: Set up for 2 dimensions using the following datasets:
[ c1 dist3 ]
norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (16 total):
0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol
3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol
10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol
11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol
13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (45 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 172040 of 172040)
1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142)
2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741)
3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630)
4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 74884 of 74884)
5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41559 of 41559)
6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201)
7: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 21662 of 21662)
8: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719)
9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023)
10: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4545 of 4545)
11: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3850 of 3850)
12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866)
13: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590)
14: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 13501 of 13501)
15: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487)
16: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4720 of 4720)
17: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3875 of 3875)
18: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1961 of 1961)
19: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458)
20: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072)
21: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18784 of 18784)
22: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656)
23: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3855 of 3855)
24: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3175 of 3175)
25: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041)
26: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387)
27: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 76671 of 76671)
28: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544)
29: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 48280 of 48280)
30: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868)
31: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571)
32: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10292 of 10292)
33: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7787 of 7787)
34: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482)
35: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137)
36: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062)
37: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 15117 of 15117)
38: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047)
39: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10637 of 10637)
40: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909)
41: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351)
42: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296)
43: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 86746 of 86746)
44: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 68322 of 68322)
Coordinate processing will occur on 2297543 frames.
BEGIN TRAJECTORY PROCESSING:
----- ctraj.c0 (1-172040, 1) -----
0%
----- ctraj.c1 (1-145142, 1) -----
10%
----- ctraj.c2 (1-88741, 1) -----
----- ctraj.c3 (1-77630, 1) -----
20%
----- ctraj.c4 (1-74884, 1) -----
----- ctraj.c5 (1-41559, 1) -----
----- ctraj.c0 (1-40201, 1) -----
----- ctraj.c1 (1-21662, 1) -----
----- ctraj.c2 (1-17719, 1) -----
----- ctraj.c3 (1-12023, 1) -----
30%
----- ctraj.c4 (1-4545, 1) -----
----- ctraj.c5 (1-3850, 1) -----
----- ctraj.c0 (1-50866, 1) -----
----- ctraj.c1 (1-18590, 1) -----
----- ctraj.c2 (1-13501, 1) -----
----- ctraj.c3 (1-6487, 1) -----
----- ctraj.c4 (1-4720, 1) -----
----- ctraj.c5 (1-3875, 1) -----
----- ctraj.c6 (1-1961, 1) -----
----- ctraj.c0 (1-49458, 1) -----
----- ctraj.c1 (1-19072, 1) -----
----- ctraj.c2 (1-18784, 1) -----
----- ctraj.c3 (1-5656, 1) -----
----- ctraj.c4 (1-3855, 1) -----
----- ctraj.c5 (1-3175, 1) -----
----- ctraj.c0 (1-273041, 1) -----
40% 50%
----- ctraj.c1 (1-134387, 1) -----
----- ctraj.c2 (1-76671, 1) -----
60%
----- ctraj.c3 (1-67544, 1) -----
----- ctraj.c4 (1-48280, 1) -----
----- ctraj.c0 (1-55868, 1) -----
----- ctraj.c1 (1-18571, 1) -----
----- ctraj.c2 (1-10292, 1) -----
----- ctraj.c3 (1-7787, 1) -----
----- ctraj.c4 (1-7482, 1) -----
----- ctraj.c0 (1-36137, 1) -----
70%
----- ctraj.c1 (1-27062, 1) -----
----- ctraj.c2 (1-15117, 1) -----
----- ctraj.c3 (1-11047, 1) -----
----- ctraj.c4 (1-10637, 1) -----
----- ctraj.c0 (1-225909, 1) -----
80%
----- ctraj.c1 (1-126351, 1) -----
----- ctraj.c2 (1-90296, 1) -----
90%
----- ctraj.c3 (1-86746, 1) -----
----- ctraj.c4 (1-68322, 1) -----
100% Complete.
Read 2297543 frames and processed 2297543 frames.
TIME: Avg. throughput= 1023207.5610 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-py.gnu norm]
Calculating bins from min=-180 max=180 step=0.5.
Dim c1: -180.000000->180.000000, step 0.500000, 720 bins.
Calculating bins from min=0 max=10 step=0.01.
Dim dist3: 0.000000->10.000000, step 0.010000, 1000 bins.
Hist: 2297543 data points in each dimension.
Hist: Allocating histogram, total bins = 720000
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 2.29754e+06
TIME: Analyses took 0.0526 seconds.
DATASETS (3 total):
dist3 "dist3" (double, distance), size is 2297543
c1 "c1" (double, torsion(chin)), size is 2297543
Hist_00018 "Hist_00018" (double matrix), size is 720000
DATAFILES (1 total):
2dhist_c1_dist3-py.gnu (Gnuplot File): Hist_00018
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 2.2454 s ( 67.25%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0526 s ( 1.58%)
TIME: Data File Write : 1.0406 s ( 31.17%)
TIME: Other : 0.0002 s ( 0.00%)
TIME: Run Total 3.3389 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 6.9617 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.