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)
              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

       -[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

       2018, GROMACS development team

2018.1                                            Mar 21, 2018                                     GMX-ROTACF(1)