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)