CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 12/04/15 16:15:22
| Available memory: 979.938 MB
INPUT: Reading Input from file pt-analysis1.in
[parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr]
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[trajin ../ctraj.c2]
Reading '../ctraj.c2' 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 ]
Reference mask: [:1,2&!@H*](43)
RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted.
[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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, 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@N9 :1@C4 type chin]
DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4]
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@N9 :2@C4 type chin]
DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4]
Output range is -180 to 180 degrees.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES:
0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111593 of 111593)
Coordinate processing will occur on 111593 frames.
REFERENCE FRAMES (1 total):
0: [a-form]:1
Active reference frame for distance-based masks is '[a-form]:1'
TIME: Run Initialization took 0.0001 seconds.
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*](43)
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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 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@N9 :1@C4 type chin]
[:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](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@N9 :2@C4 type chin]
[:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1)
----- ctraj.c2 (1-111593, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 111593 frames and processed 111593 frames.
TIME: Trajectory processing: 0.9064 s
TIME: Avg. throughput= 123117.8122 frames / second.
ACTION OUTPUT:
DATASETS:
16 data sets:
noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb' 67 atoms
rms_2_aform "rms_2_aform" (double, rms), size is 111593
dist_sugar_ox "dist_sugar_ox" (double, distance), size is 111593
dist_N3-O5p "dist_N3-O5p" (double, distance), size is 111593
COM "COM" (double, distance), size is 111593
g1 "g1" (double, torsion(gamma)), size is 111593
d1 "d1" (double, torsion(delta)), size is 111593
e1 "e1" (double, torsion(epsilon)), size is 111593
z1 "z1" (double, torsion(zeta)), size is 111593
c1 "c1" (double, torsion(chin)), size is 111593
a2 "a2" (double, torsion(alpha)), size is 111593
b2 "b2" (double, torsion(beta)), size is 111593
g2 "g2" (double, torsion(gamma)), size is 111593
d2 "d2" (double, torsion(delta)), size is 111593
c2 "c2" (double, torsion(chin)), size is 111593
---------- RUN END ---------------------------------------------------
[avg rms_2_aform out avg-rmsd-all.dat]
AVERAGE: Calculating average of 1 data sets.
Writing results 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_a2-hist.dat name gamma_1 norm]
Hist: dihed_a2-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 -------------------------------------------------
Warning: No actions/output trajectories specified.
ANALYSIS: Performing 16 analyses:
0: [avg rms_2_aform out avg-rmsd-all.dat]
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: 111593 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 111593
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: 111593 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Warning: Frame 21888 Coordinates out of bounds (-1)
Warning: Frame 24949 Coordinates out of bounds (-1)
Warning: Frame 48903 Coordinates out of bounds (-1)
Warning: Frame 52402 Coordinates out of bounds (-1)
Warning: Frame 56629 Coordinates out of bounds (-1)
Warning: Frame 67019 Coordinates out of bounds (-1)
Warning: Frame 67024 Coordinates out of bounds (-1)
Warning: Frame 67602 Coordinates out of bounds (-1)
Warning: Frame 67705 Coordinates out of bounds (-1)
Warning: Frame 70591 Coordinates out of bounds (-1)
Warning: Frame 74823 Coordinates out of bounds (-1)
Warning: Frame 103664 Coordinates out of bounds (-1)
Histogram: Normalizing sum of bin populations to 1.0
Sum over all bins is 111581
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
6: [hist g1,-180,180,1 out dihed_a2-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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
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: 111593 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 111593
TIME: Analyses took 0.0283 seconds.
DATASETS:
31 data sets:
noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
[a-form]:1 "[a-form]:1" (reference), size is 1 '../../../A-form.pdb' 67 atoms
rms_2_aform "rms_2_aform" (double, rms), size is 111593
dist_sugar_ox "dist_sugar_ox" (double, distance), size is 111593
dist_N3-O5p "dist_N3-O5p" (double, distance), size is 111593
COM "COM" (double, distance), size is 111593
g1 "g1" (double, torsion(gamma)), size is 111593
d1 "d1" (double, torsion(delta)), size is 111593
e1 "e1" (double, torsion(epsilon)), size is 111593
z1 "z1" (double, torsion(zeta)), size is 111593
c1 "c1" (double, torsion(chin)), size is 111593
a2 "a2" (double, torsion(alpha)), size is 111593
b2 "b2" (double, torsion(beta)), size is 111593
g2 "g2" (double, torsion(gamma)), size is 111593
d2 "d2" (double, torsion(delta)), size is 111593
c2 "c2" (double, torsion(chin)), size is 111593
RMSD "RMSD" (double), size is 50
CoM "CoM" (double), size is 100
Hist_00018 "Hist_00018" (double), size is 100
Hist_00019 "Hist_00019" (double), size is 100
Hist_00020 "Hist_00020" (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:
rmsd-hist.dat (Standard Data File): RMSD
COM-hist.dat (Standard Data File): CoM
distO2O4-hist.dat (Standard Data File): Hist_00018
distN3-O5p-hist.dat (Standard Data File): Hist_00019
2dhist_rms-dist.gnu (Gnuplot File): Hist_00020
dihed_a2-hist.dat (Standard Data File): gamma_1 alpha_2
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_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
avg-rmsd-all.dat (DataSet Average)
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.9910 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.