Provided by: gromacs-data_5.1.2-1ubuntu1_all 
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