gmx-rotacf(1) GROMACS Manual gmx-rotacf(1)NAMEgmx-rotacf - Calculate the rotational correlation function for mole‐
cules
SYNOPSIS
gmx rotacf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-nice <int>] [-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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input)
Index file
-o [<.xvg>] (rotacf.xvg) (Output)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-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> (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, vac, exp5, exp7, exp9, erf‐
fit
-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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-rotacf(1)
