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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 sup- ports both vectors defined by two positions and normals of planes de- fined 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 op- tions '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 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 po- sition 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 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: xmgrace, xmgr, none -[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 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-GANGLE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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