1GMX-GANGLE(1) GROMACS GMX-GANGLE(1)
2
6 gmx-gangle - Calculate angles
7
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
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 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 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 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 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 With -g2 z, -group2 is not necessary, and angles between the first vec‐
51 tors and the positive Z axis are calculated.
52 With -g2 t0, -group2 is not necessary, and angles are calculated from
54 the vectors as they are in the first frame.
55 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
63 Options to specify input files:
64 -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
66 Input trajectory or single configuration: xtc trr cpt gro g96
67 pdb tng
68 -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
70 Input structure: tpr gro g96 pdb brk ent
71 -n [<.ndx>] (index.ndx) (Optional)
73 Extra index groups
74 Options to specify output files:
76 -oav [<.xvg>] (angaver.xvg) (Optional)
78 Average angles as a function of time
79 -oall [<.xvg>] (angles.xvg) (Optional)
81 All angles as a function of time
82 -oh [<.xvg>] (anghist.xvg) (Optional)
84 Histogram of the angles
85 Other options:
87 -b <time> (0)
89 First frame (ps) to read from trajectory
90 -e <time> (0)
92 Last frame (ps) to read from trajectory
93 -dt <time> (0)
95 Only use frame if t MOD dt == first time (ps)
96 -tu <enum> (ps)
98 Unit for time values: fs, ps, ns, us, ms, s
99 -fgroup <selection>
101 Atoms stored in the trajectory file (if not set, assume first N
102 atoms)
103 -xvg <enum> (xmgrace)
105 Plot formatting: xmgrace, xmgr, none
106 -[no]rmpbc (yes)
108 Make molecules whole for each frame
109 -[no]pbc (yes)
111 Use periodic boundary conditions for distance calculation
112 -sf <file>
114 Provide selections from files
115 -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 -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 -g1 <enum> (angle)
129 Type of analysis/first vector group: angle, dihedral, vector,
130 plane
131 -g2 <enum> (none)
133 Type of second vector group: none, vector, plane, t0, z, sphnorm
134 -binw <real> (1)
136 Binwidth for -oh in degrees
137 -group1 <selection>
139 First analysis/vector selection
140 -group2 <selection>
142 Second analysis/vector selection
143
145 gmx(1)
146 More information about GROMACS is available at <‐
148 http://www.gromacs.org/>.
149
151 2022, GROMACS development team
1522022.3 Sep 02, 2022 GMX-GANGLE(1)