gmx gangle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-oav [<.xvg>]] [-oall [<.xvg>]] [-oh [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-seltype <enum>] [-g1 <enum>] [-g2 <enum>] [-binw <real>] [-group1 <selection>] [-group2 <selection>]
gmx gangle computes different types of angles between vectors.
It supports both vectors defined by two positions and normals of
planes defined by three positions.
The z axis or the local normal of a sphere can also be used as
one of the vectors.
There are also convenience options ‘angle’ and ‘dihedral’ for
calculating bond angles and dihedrals defined by three/four
The type of the angle is specified with
should not be specified.
In this case,
-group1 should specify one or more selections,
and each should contain triplets or quartets of positions that define
the angles to be calculated.
should specify selections that contain either pairs (
or triplets (
plane) of positions. For vectors, the positions
set the endpoints of the vector, and for planes, the three positions
are used to calculate the normal of the plane. In both cases,
-g2 specifies the other vector to use (see below).
-g2 vector or
specify another set of vectors.
should specify the same number of selections. It is also allowed to
only have a single selection for one of the options, in which case
the same selection is used with each selection in the other group.
Similarly, for each selection in
-group1, the corresponding
-group2 should specify the same number of
vectors or a single vector. In the latter case, the angle is
calculated between that single vector and each vector from the other
-g2 sphnorm, each selection in
specify a single position that is the center of the sphere.
The second vector is calculated as the vector from the center to the
midpoint of the positions specified by
-group2 is not necessary, and angles
between the first vectors and the positive Z axis are calculated.
-group2 is not necessary, and angles
are calculated from the vectors as they are in the first frame.
There are three options for output:
-oav writes an xvg file with the time and the average angle
for each frame.
-oall writes all the individual angles.
-oh writes a histogram of the angles. The bin width can be
-oh, separate average/histogram is
computed for each selection in
Options to specify input files:
-f[<.xtc/.trr/…>] (traj.xtc) (Optional)
Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Extra index groups
Options to specify output files:
-oav[<.xvg>] (angaver.xvg) (Optional)
Average angles as a function of time
-oall[<.xvg>] (angles.xvg) (Optional)
All angles as a function of time
-oh[<.xvg>] (anghist.xvg) (Optional)
Histogram of the angles
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
Make molecules whole for each frame
Use periodic boundary conditions for distance calculation
Provide selections from files
Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
Type of analysis/first vector group: angle, dihedral, vector, plane
Type of second vector group: none, vector, plane, t0, z, sphnorm
Binwidth for -oh in degrees
First analysis/vector selection
Second analysis/vector selection