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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

       2019, GROMACS development team