1GMX-GANGLE(1)                       GROMACS                      GMX-GANGLE(1)
2
3
4

NAME

6       gmx-gangle - Calculate angles
7

SYNOPSIS

9          gmx gangle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                     [-oav [<.xvg>]] [-oall [<.xvg>]] [-oh [<.xvg>]]
11                     [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
12                     [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
13                     [-[no]pbc] [-sf <file>] [-selrpos <enum>]
14                     [-seltype <enum>] [-g1 <enum>] [-g2 <enum>] [-binw <real>]
15                     [-group1 <selection>] [-group2 <selection>]
16

DESCRIPTION

18       gmx gangle computes different types of angles between vectors.  It sup‐
19       ports both vectors defined by two positions and normals of  planes  de‐
20       fined  by  three positions.  The z axis or the local normal of a sphere
21       can also be used as one of the vectors.  There are also convenience op‐
22       tions  'angle' and 'dihedral' for calculating bond angles and dihedrals
23       defined by three/four positions.
24
25       The type of the angle is specified with -g1 and -g2.  If -g1  is  angle
26       or dihedral, -g2 should not be specified.  In this case, -group1 should
27       specify one or more selections, and each  should  contain  triplets  or
28       quartets of positions that define the angles to be calculated.
29
30       If  -g1 is vector or plane, -group1 should specify selections that con‐
31       tain either pairs (vector) or triplets (plane) of positions.  For  vec‐
32       tors,  the  positions  set the endpoints of the vector, and for planes,
33       the three positions are used to calculate the normal of the  plane.  In
34       both cases, -g2 specifies the other vector to use (see below).
35
36       With  -g2  vector  or  -g2 plane, -group2 should specify another set of
37       vectors. -group1 and -group2 should specify the same number  of  selec‐
38       tions.  It  is  also allowed to only have a single selection for one of
39       the options, in which case the same selection is used with each  selec‐
40       tion in the other group.  Similarly, for each selection in -group1, the
41       corresponding selection in -group2 should specify the  same  number  of
42       vectors or a single vector. In the latter case, the angle is calculated
43       between that single vector and each vector from the other selection.
44
45       With -g2 sphnorm, each selection in -group2 should specify a single po‐
46       sition  that  is the center of the sphere.  The second vector is calcu‐
47       lated as the vector from the center to the midpoint  of  the  positions
48       specified by -group1.
49
50       With -g2 z, -group2 is not necessary, and angles between the first vec‐
51       tors and the positive Z axis are calculated.
52
53       With -g2 t0, -group2 is not necessary, and angles are  calculated  from
54       the vectors as they are in the first frame.
55
56       There  are  three  options for output: -oav writes an xvg file with the
57       time and the average angle for each frame.  -oall writes all the  indi‐
58       vidual angles.  -oh writes a histogram of the angles. The bin width can
59       be set with -binw.  For -oav and  -oh,  separate  average/histogram  is
60       computed for each selection in -group1.
61

OPTIONS

63       Options to specify input files:
64
65       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
66              Input  trajectory  or  single configuration: xtc trr cpt gro g96
67              pdb tng
68
69       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
70              Input structure: tpr gro g96 pdb brk ent
71
72       -n [<.ndx>] (index.ndx) (Optional)
73              Extra index groups
74
75       Options to specify output files:
76
77       -oav [<.xvg>] (angaver.xvg) (Optional)
78              Average angles as a function of time
79
80       -oall [<.xvg>] (angles.xvg) (Optional)
81              All angles as a function of time
82
83       -oh [<.xvg>] (anghist.xvg) (Optional)
84              Histogram of the angles
85
86       Other options:
87
88       -b <time> (0)
89              First frame (ps) to read from trajectory
90
91       -e <time> (0)
92              Last frame (ps) to read from trajectory
93
94       -dt <time> (0)
95              Only use frame if t MOD dt == first time (ps)
96
97       -tu <enum> (ps)
98              Unit for time values: fs, ps, ns, us, ms, s
99
100       -fgroup <selection>
101              Atoms stored in the trajectory file (if not set, assume first  N
102              atoms)
103
104       -xvg <enum> (xmgrace)
105              Plot formatting: xmgrace, xmgr, none
106
107       -[no]rmpbc (yes)
108              Make molecules whole for each frame
109
110       -[no]pbc (yes)
111              Use periodic boundary conditions for distance calculation
112
113       -sf <file>
114              Provide selections from files
115
116       -selrpos <enum> (atom)
117              Selection  reference positions: atom, res_com, res_cog, mol_com,
118              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
119              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
120              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
121
122       -seltype <enum> (atom)
123              Default selection  output  positions:  atom,  res_com,  res_cog,
124              mol_com,  mol_cog,  whole_res_com, whole_res_cog, whole_mol_com,
125              whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
126              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
127
128       -g1 <enum> (angle)
129              Type  of  analysis/first  vector group: angle, dihedral, vector,
130              plane
131
132       -g2 <enum> (none)
133              Type of second vector group: none, vector, plane, t0, z, sphnorm
134
135       -binw <real> (1)
136              Binwidth for -oh in degrees
137
138       -group1 <selection>
139              First analysis/vector selection
140
141       -group2 <selection>
142              Second analysis/vector selection
143

SEE ALSO

145       gmx(1)
146
147       More    information    about    GROMACS    is    available    at     <‐
148       http://www.gromacs.org/>.
149
151       2022, GROMACS development team
152
153
154
155
1562022.3                           Sep 02, 2022                    GMX-GANGLE(1)
Impressum