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gmx-rotacf(1)                   GROMACS Manual                   gmx-rotacf(1)

NAME
       gmx-rotacf - Calculate the rotational correlation function for
       molecules

SYNOPSIS
       gmx rotacf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
                  [-n [<.ndx>]] [-o [<.xvg>]] [-nice <int>] [-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 and output files:

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

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

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

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

       Other options:

       -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]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, vac, exp5, exp7, exp9,
       erffit

       -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/>.

VERSION 5.0.6                                                    gmx-rotacf(1)