Provided by: gromacs-data_4.6.5-1build1_all bug


       g_angle - calculates distributions and correlations for angles and dihedrals

       VERSION 4.6.5


       g_angle  -f  traj.xtc  -n  angle.ndx  -od  angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot
       dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -[no]version -nice int -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  -ncskip  int
       -beginfit real -endfit real


        g_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,  g_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

       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.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n angle.ndx Input
        Index file

       -od angdist.xvg Output
        xvgr/xmgr file

       -ov angaver.xvg Output, Opt.
        xvgr/xmgr file

       -of dihfrac.xvg Output, Opt.
        xvgr/xmgr file

       -ot dihtrans.xvg Output, Opt.
        xvgr/xmgr file

       -oh trhisto.xvg Output, Opt.
        xvgr/xmgr file

       -oc dihcorr.xvg Output, Opt.
        xvgr/xmgr file

       -or traj.trr Output, Opt.
        Trajectory in portable xdr format


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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 when t MOD dt = first time (ps)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -type enum angle
        Type of angle to analyse:  angle,  dihedral,  improper or  ryckaert-bellemans

        Plot  all angles separately in the averages file, in the order of appearance in the index

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

        Print dihedral angles modulo 360 degrees

        Use Chandler correlation function (N[trans] =  1,  N[gauche]  =  0)  rather  than  cosine
       correlation function. Trans is defined as phi  -60 or phi  60.

        Average the correlation functions for the individual angles/dihedrals

       -acflen int -1
        Length of the ACF, default is half the number of frames

        Normalize ACF

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

       -fitfn enum none
        Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

       -ncskip int 0
        Skip this many points in the output file of correlation functions

       -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


       - Counting transitions only works for dihedrals with multiplicity 3



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               g_angle(1)