FreeBSD Manual Pages
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)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=gmx-rotacf&sektion=1&manpath=FreeBSD+Ports+14.3.quarterly>