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

       2020, GROMACS development team