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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 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:

Trajectory: xtc trr cpt gro g96 pdb tng
Portable xdr run input file
Index file

Options to specify output files:

xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
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
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end

SEE ALSO

gmx(1)

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COPYRIGHT

2024, GROMACS development team

October 31, 2024 2024.4