CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 18:20:57
| Available memory: 3.877 GB
INPUT: Reading input from 'pt-analysis1.in'
[parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr]
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[trajin ../ctraj.c0]
Reading '../ctraj.c0' as Amber NetCDF
[reference ../../../A-form.pdb [a-form]]
Reading '../../../A-form.pdb' as PDB
Setting active reference for distance-based masks: 'A-form.pdb'
[rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and translated.
[distance dist_sugar_ox :1@O2' :2@O4']
DISTANCE: :1@O2' to :2@O4', center of mass.
[distance dist_N3-O5p :1@N3 :1@O5']
DISTANCE: :1@N3 to :1@O5', center of mass.
[distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3']
Output range is -180 to 180 degrees.
[dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3']
Output range is -180 to 180 degrees.
[dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P]
Output range is -180 to 180 degrees.
[dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5']
Output range is -180 to 180 degrees.
[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.
[dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5']
Output range is -180 to 180 degrees.
[dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4']
Output range is -180 to 180 degrees.
[dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3']
Output range is -180 to 180 degrees.
[dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3']
Output range is -180 to 180 degrees.
[dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2]
Output range is -180 to 180 degrees.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: noWAt.topo.hmr, 60 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 36137 of 36137)
Coordinate processing will occur on 36137 frames.
REFERENCE FRAMES (1 total):
0: [a-form]:1
Active reference frame for distance-based masks is '[a-form]:1'
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions):
0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass]
Target mask: [:1,2&!@H*](37)
Reference mask: [:1,2&!@H*](37)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
1: [distance dist_sugar_ox :1@O2' :2@O4']
:1@O2' (1 atoms) to :2@O4' (1 atoms), imaged.
2: [distance dist_N3-O5p :1@N3 :1@O5']
:1@N3 (1 atoms) to :1@O5' (1 atoms), imaged.
3: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma]
[:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1)
5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta]
[:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1)
6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon]
[:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1)
7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta]
[:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1)
8: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi]
[:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1)
9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha]
[:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1)
10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta]
[:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1)
11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma]
[:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1)
12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta]
[:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1)
13: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi]
[:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1)
----- ctraj.c0 (1-36137, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 36137 frames and processed 36137 frames.
TIME: Avg. throughput= 109481.5102 frames / second.
ACTION OUTPUT:
DATASETS (14 total):
rms_2_aform "rms_2_aform" (double, rms), size is 36137
dist_sugar_ox "dist_sugar_ox" (double, distance), size is 36137
dist_N3-O5p "dist_N3-O5p" (double, distance), size is 36137
COM "COM" (double, distance), size is 36137
g1 "g1" (double, torsion(gamma)), size is 36137
d1 "d1" (double, torsion(delta)), size is 36137
e1 "e1" (double, torsion(epsilon)), size is 36137
z1 "z1" (double, torsion(zeta)), size is 36137
c1 "c1" (double, torsion(chin)), size is 36137
a2 "a2" (double, torsion(alpha)), size is 36137
b2 "b2" (double, torsion(beta)), size is 36137
g2 "g2" (double, torsion(gamma)), size is 36137
d2 "d2" (double, torsion(delta)), size is 36137
c2 "c2" (double, torsion(chin)), size is 36137
RUN TIMING:
TIME: Init : 0.0001 s ( 0.02%)
TIME: Trajectory Process : 0.3301 s ( 99.96%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.3302 s
---------- RUN END ---------------------------------------------------
[avg rms_2_aform out avg-rmsd-all.dat]
AVERAGE: Calculating average of 1 data sets.
Data set base name 'AVERAGE_00016'
Output to to 'avg-rmsd-all.dat'
[hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets:
[ rms_2_aform ]
norm: Sum over bins will be normalized to 1.0.
[hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets:
[ COM ]
norm: Sum over bins will be normalized to 1.0.
[hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets:
[ dist_sugar_ox ]
norm: Sum over bins will be normalized to 1.0.
[hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets:
[ dist_N3-O5p ]
norm: Sum over bins will be normalized to 1.0.
[hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets:
[ rms_2_aform dist_sugar_ox ]
norm: Sum over bins will be normalized to 1.0.
[hist g1,-180,180,1 out dihed_g1-hist.dat name gamma_1 norm]
Hist: dihed_g1-hist.dat: Set up for 1 dimensions using the following datasets:
[ g1 ]
norm: Sum over bins will be normalized to 1.0.
[hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets:
[ d1 ]
norm: Sum over bins will be normalized to 1.0.
[hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets:
[ e1 ]
norm: Sum over bins will be normalized to 1.0.
[hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets:
[ z1 ]
norm: Sum over bins will be normalized to 1.0.
[hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets:
[ c1 ]
norm: Sum over bins will be normalized to 1.0.
[hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets:
[ a2 ]
norm: Sum over bins will be normalized to 1.0.
[hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets:
[ b2 ]
norm: Sum over bins will be normalized to 1.0.
[hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets:
[ g2 ]
norm: Sum over bins will be normalized to 1.0.
[hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets:
[ d2 ]
norm: Sum over bins will be normalized to 1.0.
[hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets:
[ c2 ]
norm: Sum over bins will be normalized to 1.0.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: noWAt.topo.hmr, 60 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 36137 of 36137)
Coordinate processing will occur on 36137 frames.
REFERENCE FRAMES (1 total):
0: [a-form]:1
Active reference frame for distance-based masks is '[a-form]:1'
BEGIN TRAJECTORY PROCESSING:
----- ctraj.c0 (1-36137, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 36137 frames and processed 36137 frames.
TIME: Avg. throughput= 320247.0733 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 16 analyses:
0: [avg rms_2_aform out avg-rmsd-all.dat]
1: rms_2_aform
1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm]
Calculating bins from min=0 max=5 step=0.1.
Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 50
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm]
Calculating bins from min=0 max=10 step=0.1.
Dim COM: 0.000000->10.000000, step 0.100000, 100 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Warning: Frame 1489 Coordinates out of bounds (-1)
Warning: Frame 2247 Coordinates out of bounds (-1)
Warning: Frame 2508 Coordinates out of bounds (-1)
Warning: Frame 3317 Coordinates out of bounds (-1)
Warning: Frame 3444 Coordinates out of bounds (-1)
Warning: Frame 4547 Coordinates out of bounds (-1)
Warning: Frame 6264 Coordinates out of bounds (-1)
Warning: Frame 6265 Coordinates out of bounds (-1)
Warning: Frame 9608 Coordinates out of bounds (-1)
Warning: Frame 10950 Coordinates out of bounds (-1)
Warning: Frame 13884 Coordinates out of bounds (-1)
Warning: Frame 14987 Coordinates out of bounds (-1)
Warning: Frame 15866 Coordinates out of bounds (-1)
Warning: Frame 16099 Coordinates out of bounds (-1)
Warning: Frame 16233 Coordinates out of bounds (-1)
Warning: Frame 16791 Coordinates out of bounds (-1)
Warning: Frame 18159 Coordinates out of bounds (-1)
Warning: Frame 18299 Coordinates out of bounds (-1)
Warning: Frame 18605 Coordinates out of bounds (-1)
Warning: Frame 19650 Coordinates out of bounds (-1)
Warning: Frame 19653 Coordinates out of bounds (-1)
Warning: Frame 20134 Coordinates out of bounds (-1)
Warning: Frame 20210 Coordinates out of bounds (-1)
Warning: Frame 20931 Coordinates out of bounds (-1)
Warning: Frame 21815 Coordinates out of bounds (-1)
Warning: Frame 22214 Coordinates out of bounds (-1)
Warning: Frame 23634 Coordinates out of bounds (-1)
Warning: Frame 24028 Coordinates out of bounds (-1)
Warning: Frame 24165 Coordinates out of bounds (-1)
Warning: Frame 24408 Coordinates out of bounds (-1)
Warning: Frame 25428 Coordinates out of bounds (-1)
Warning: Frame 27886 Coordinates out of bounds (-1)
Warning: Frame 27996 Coordinates out of bounds (-1)
Warning: Frame 28081 Coordinates out of bounds (-1)
Warning: Frame 28818 Coordinates out of bounds (-1)
Warning: Frame 29294 Coordinates out of bounds (-1)
Warning: Frame 29296 Coordinates out of bounds (-1)
Warning: Frame 29603 Coordinates out of bounds (-1)
Warning: Frame 29677 Coordinates out of bounds (-1)
Warning: Frame 32071 Coordinates out of bounds (-1)
Warning: Frame 32727 Coordinates out of bounds (-1)
Warning: Frame 34235 Coordinates out of bounds (-1)
Warning: Frame 35286 Coordinates out of bounds (-1)
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36094
3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm]
Calculating bins from min=0 max=10 step=0.1.
Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm]
Calculating bins from min=0 max=10 step=0.1.
Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm]
Calculating bins from min=0 max=5 step=0.1.
Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins.
Calculating bins from min=0 max=10 step=0.1.
Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 5000
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
6: [hist g1,-180,180,1 out dihed_g1-hist.dat name gamma_1 norm]
Calculating bins from min=-180 max=180 step=1.
Dim g1: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm]
Calculating bins from min=-180 max=180 step=1.
Dim d1: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm]
Calculating bins from min=-180 max=180 step=1.
Dim e1: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm]
Calculating bins from min=-180 max=180 step=1.
Dim z1: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm]
Calculating bins from min=-180 max=180 step=1.
Dim c1: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm]
Calculating bins from min=-180 max=180 step=1.
Dim a2: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm]
Calculating bins from min=-180 max=180 step=1.
Dim b2: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm]
Calculating bins from min=-180 max=180 step=1.
Dim g2: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm]
Calculating bins from min=-180 max=180 step=1.
Dim d2: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm]
Calculating bins from min=-180 max=180 step=1.
Dim c2: -180.000000->180.000000, step 1.000000, 360 bins.
Hist: 36137 data points in each dimension.
Hist: Allocating histogram, total bins = 360
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 36137
TIME: Analyses took 0.0119 seconds.
DATASETS (36 total):
rms_2_aform "rms_2_aform" (double, rms), size is 36137
dist_sugar_ox "dist_sugar_ox" (double, distance), size is 36137
dist_N3-O5p "dist_N3-O5p" (double, distance), size is 36137
COM "COM" (double, distance), size is 36137
g1 "g1" (double, torsion(gamma)), size is 36137
d1 "d1" (double, torsion(delta)), size is 36137
e1 "e1" (double, torsion(epsilon)), size is 36137
z1 "z1" (double, torsion(zeta)), size is 36137
c1 "c1" (double, torsion(chin)), size is 36137
a2 "a2" (double, torsion(alpha)), size is 36137
b2 "b2" (double, torsion(beta)), size is 36137
g2 "g2" (double, torsion(gamma)), size is 36137
d2 "d2" (double, torsion(delta)), size is 36137
c2 "c2" (double, torsion(chin)), size is 36137
AVERAGE_00016[avg] "AVERAGE_00016[avg]" (double), size is 1
AVERAGE_00016[sd] "AVERAGE_00016[sd]" (double), size is 1
AVERAGE_00016[ymin] "AVERAGE_00016[ymin]" (double), size is 1
AVERAGE_00016[ymax] "AVERAGE_00016[ymax]" (double), size is 1
AVERAGE_00016[yminidx] "AVERAGE_00016[yminidx]" (integer), size is 1
AVERAGE_00016[ymaxidx] "AVERAGE_00016[ymaxidx]" (integer), size is 1
AVERAGE_00016[names] "AVERAGE_00016[names]" (string), size is 1
RMSD "RMSD" (double), size is 50
CoM "CoM" (double), size is 100
Hist_00025 "Hist_00025" (double), size is 100
Hist_00026 "Hist_00026" (double), size is 100
Hist_00027 "Hist_00027" (double matrix), size is 5000
gamma_1 "gamma_1" (double), size is 360
delta_1 "delta_1" (double), size is 360
epsilon_1 "epsilon_1" (double), size is 360
zeta_1 "zeta_1" (double), size is 360
chi_1 "chi_1" (double), size is 360
alpha_2 "alpha_2" (double), size is 360
beta_2 "beta_2" (double), size is 360
gamma_2 "gamma_2" (double), size is 360
delta_2 "delta_2" (double), size is 360
chi_2 "chi_2" (double), size is 360
DATAFILES (16 total):
avg-rmsd-all.dat (Standard Data File): AVERAGE_00016[avg] AVERAGE_00016[sd] AVERAGE_00016[ymin] AVERAGE_00016[ymax] AVERAGE_00016[yminidx] AVERAGE_00016[ymaxidx] AVERAGE_00016[names]
rmsd-hist.dat (Standard Data File): RMSD
COM-hist.dat (Standard Data File): CoM
distO2O4-hist.dat (Standard Data File): Hist_00025
distN3-O5p-hist.dat (Standard Data File): Hist_00026
2dhist_rms-dist.gnu (Gnuplot File): Hist_00027
dihed_g1-hist.dat (Standard Data File): gamma_1
dihed_d1-hist.dat (Standard Data File): delta_1
dihed_e1-hist.dat (Standard Data File): epsilon_1
dihed_z1-hist.dat (Standard Data File): zeta_1
dihed_c1-hist.dat (Standard Data File): chi_1
dihed_a2-hist.dat (Standard Data File): alpha_2
dihed_b2-hist.dat (Standard Data File): beta_2
dihed_g2-hist.dat (Standard Data File): gamma_2
dihed_d2-hist.dat (Standard Data File): delta_2
dihed_c2-hist.dat (Standard Data File): chi_2
RUN TIMING:
TIME: Init : 0.0001 s ( 0.01%)
TIME: Trajectory Process : 0.1128 s ( 8.58%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0119 s ( 0.91%)
TIME: Data File Write : 1.1901 s ( 90.50%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 1.3150 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2.4550 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.