NAME

       gmx-rotacf - Calculate the rotational correlation function for molecules

SYNOPSIS

          gmx rotacf [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
                     [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
                     [-[no]w] [-xvg <enum>] [-[no]d] [-[no]aver]
                     [-acflen <int>] [-[no]normalize] [-P <enum>]
                     [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

DESCRIPTION

       gmx  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

       gmx  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.

OPTIONS

       Options to specify input files:

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

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

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

       Options to specify output files:

       -o [<.xvg>] (rotacf.xvg)
              xvgr/xmgr file

       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 when t MOD dt = first time (ps)

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

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

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

       -[no]aver (yes)
              Average over molecules

       -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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team