GMX-ROTACF(1) GROMACS GMX-ROTACF(1) 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 mat- ter. Optionally, by invoking the -d switch, you can calculate the rota- tional 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 -be- ginfit 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-pa- rameter exponential. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) Trajectory: xtc trr cpt gro g96 pdb tng h5md -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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-ROTACF(1)
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