gmx-gangle(1) GROMACS Manual gmx-gangle(1)NAMEgmx-gangle - Calculate angles
SYNOPSIS
gmx gangle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-oav [<.xvg>]] [-oall [<.xvg>]]
[-oh [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-tu <enum>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc]
[-sf <file>] [-selrpos <enum>] [-g1 <enum>] [-g2 <enum>]
[-binw <real>] [-group1 <selection>] [-group2 <selection>]
DESCRIPTION
gmx gangle computes different types of angles between vectors. It sup‐
ports 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 dihe‐
drals defined by three/four positions.
The type of the angle is specified with -g1 and -g2. If -g1 is angle or
dihedral, -g2 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.
If -g1 is vector or plane, -group1 should specify selections that con‐
tain either pairs (vector) or triplets (plane) of positions. For vec‐
tors, 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).
With -g2 vector or -g2 plane, -group2 should specify another set of
vectors. -group1 and -group2 should specify the same number of selec‐
tions. 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 selec‐
tion in the other group. Similarly, for each selection in -group1, the
corresponding selection in -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 selection.
With -g2 sphnorm, each selection in -group2 should specify a single
position that is the center of the sphere. The second vector is calcu‐
lated as the vector from the center to the midpoint of the positions
specified by -group1.
With -g2 z, -group2 is not necessary, and angles between the first vec‐
tors and the positive Z axis are calculated.
With -g2 t0, -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 indi‐
vidual angles. -oh writes a histogram of the angles. The bin width can
be set with -binw. For -oav and -oh, separate average/histogram is com‐
puted for each selection in -group1.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Input trajectory or single configuration: xtc trr cpt trj gro g96
pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Input structure: tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Extra index groups
-oav [<.xvg>] (angaver.xvg) (Output, Optional)
Average angles as a function of time
-oall [<.xvg>] (angles.xvg) (Output, Optional)
All angles as a function of time
-oh [<.xvg>] (anghist.xvg) (Output, Optional)
Histogram of the angles
Other options:
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame if t MOD dt == first time (ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
Plot formatting: none, xmgrace, xmgr
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
-sf <file>
Provide selections from files
-selrpos <enum> (atom)
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
-g1 <enum> (angle)
Type of analysis/first vector group: angle, dihedral, vector, plane
-g2 <enum> (none)
Type of second vector group: none, vector, plane, t0, z, sphnorm
-binw <real> (1)
Binwidth for -oh in degrees
-group1 <selection>
First analysis/vector selection
-group2 <selection>
Second analysis/vector selection
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-gangle(1)
