Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-angle - Calculate distributions and correlations for angles and dihedrals

SYNOPSIS

          gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]
                    [-ov [<.xvg>]] [-of [<.xvg>]] [-ot [<.xvg>]] [-oh [<.xvg>]]
                    [-oc [<.xvg>]] [-or [<.trr>]] [-b <time>] [-e <time>]
                    [-dt <time>] [-[no]w] [-xvg <enum>] [-type <enum>]
                    [-[no]all] [-binwidth <real>] [-[no]periodic]
                    [-[no]chandler] [-[no]avercorr] [-acflen <int>]
                    [-[no]normalize] [-P <enum>] [-fitfn <enum>]
                    [-beginfit <real>] [-endfit <real>]

DESCRIPTION

       gmx angle computes the angle distribution for a number of angles or dihedrals.

       With  option  -ov,  you  can  plot the average angle of a group of angles as a function of
       time. With the -all option, the first graph is the average and the rest are the individual
       angles.

       With  the  -of option, gmx angle also calculates the fraction of trans dihedrals (only for
       dihedrals) as function of time, but this is probably only fun for a select few.

       With option -oc, a dihedral correlation function is calculated.

       It should be noted that the index file must contain  atom  triplets  for  angles  or  atom
       quadruplets for dihedrals.  If this is not the case, the program will crash.

       With  option  -or, a trajectory file is dumped containing cos and sin of selected dihedral
       angles, which subsequently can be used as input for a principal components analysis  using
       gmx covar.

       Option  -ot  plots  when transitions occur between dihedral rotamers of multiplicity 3 and
       -oh records a histogram  of  the  times  between  such  transitions,  assuming  the  input
       trajectory frames are equally spaced in time.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (angle.ndx)
              Index file

       Options to specify output files:

       -od [<.xvg>] (angdist.xvg)
              xvgr/xmgr file

       -ov [<.xvg>] (angaver.xvg) (Optional)
              xvgr/xmgr file

       -of [<.xvg>] (dihfrac.xvg) (Optional)
              xvgr/xmgr file

       -ot [<.xvg>] (dihtrans.xvg) (Optional)
              xvgr/xmgr file

       -oh [<.xvg>] (trhisto.xvg) (Optional)
              xvgr/xmgr file

       -oc [<.xvg>] (dihcorr.xvg) (Optional)
              xvgr/xmgr file

       -or [<.trr>] (traj.trr) (Optional)
              Trajectory in portable xdr format

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -type <enum> (angle)
              Type of angle to analyse: angle, dihedral, improper, ryckaert-bellemans

       -[no]all (no)
              Plot  all angles separately in the averages file, in the order of appearance in the
              index file.

       -binwidth <real> (1)
              binwidth (degrees) for calculating the distribution

       -[no]periodic (yes)
              Print dihedral angles modulo 360 degrees

       -[no]chandler (no)
              Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than  cosine
              correlation function. Trans is defined as phi < -60 or phi > 60.

       -[no]avercorr (no)
              Average the correlation functions for the individual angles/dihedrals

       -acflen <int> (-1)
              Length of the ACF, default is half the number of frames

       -[no]normalize (yes)
              Normalize ACF

       -P <enum> (0)
              Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

       -fitfn <enum> (none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -beginfit <real> (0)
              Time where to begin the exponential fit of the correlation function

       -endfit <real> (-1)
              Time  where to end the exponential fit of the correlation function, -1 is until the
              end

KNOWN ISSUES

       · Counting transitions only works for dihedrals with multiplicity 3

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team