NAME

       g_rotacf - calculates the rotational correlation function for molecules

       VERSION 4.6.5

SYNOPSIS

       g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int
       -b time -e time -dt time -[no]w -xvg enum -[no]d -[no]aver -acflen int  -[no]normalize  -P
       enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION

         g_rotacf  calculates  the  rotational  correlation function for molecules. Atom triplets
       (i,j,k) must be given in the index file, defining two vectors ij and  jk.  The  rotational
       ACF  is  calculated  as  the  autocorrelation function of the vector n = ij x jk, i.e. the
       cross product of the two vectors.  Since three atoms span a plane, the order of the  three
       atoms  does  not  matter.  Optionally,  by  invoking the  -d switch, you can calculate the
       rotational correlation function for linear molecules by specifying atom pairs (i,j) in the
       index file.

       EXAMPLES

        g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit
       20.0

       This will calculate the rotational correlation  function  using  a  first  order  Legendre
       polynomial  of  the  angle of a vector defined by the index file. The correlation function
       will be fitted from 2.5 ps until 20.0 ps to a two-parameter exponential.

FILES

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

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input
        Index file

       -o rotacf.xvg Output
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        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)

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

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

       -[no]dno
        Use index doublets (vectors) for correlation function instead of triplets (planes)

       -[no]averyes
        Average over molecules

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

       -[no]normalizeyes
        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

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                              g_rotacf(1)