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GMX-ROTACF(1)			    GROMACS			 GMX-ROTACF(1)

NAME
       gmx-rotacf  -  Calculate	 the rotational	correlation function for mole-
       cules

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	 mole-
       cules.  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 autocor-
       relation	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 func-
	      tion

       -endfit <real> (-1)
	      Time where to end	the exponential	fit of the  correlation	 func-
	      tion, -1 is until	the end

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025			 GMX-ROTACF(1)

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