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GMX-GANGLE(1) GROMACS GMX-GANGLE(1)

NAME

gmx-gangle - Calculate angles

SYNOPSIS

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>]


DESCRIPTION

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 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 contain either pairs ( vector) 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).
With -g2 vector or -g2 plane, -group2 should specify another set of vectors. -group1 and -group2 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 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 calculated 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 vectors 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 individual angles. -oh writes a histogram of the angles. The bin width can be set with -binw. For -oav and -oh, separate average/histogram is computed for each selection in -group1.

OPTIONS

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)
Input structure: tpr gro g96 pdb brk ent
-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

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
-fgroup <selection>
Atoms stored in the trajectory file (if not set, assume first N atoms)
-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
-seltype <enum> (atom)
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
-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 ALSO

gmx(1)
More information about GROMACS is available at < http://www.gromacs.org/>.

COPYRIGHT

2018, GROMACS development team
June 14, 2018 2018.2