NAME
g_rotacf - calculates the rotational correlation function for molecules
VERSION 4.0.1
SYNOPSIS
g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h
-nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]d -[no]aver
-acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit
real -endfit real
DESCRIPTION
g_rotacf calculates the rotational correlation function for molecules.
Three atoms (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, controlled by the -d
switch, you can calculate the rotational correlation function for
linear molecules by specifying two atoms (i,j) in the index file.
EXAMPLES
g_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 till 20.0 ps
to a two parameter exponential
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input
Index file
-o rotacf.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-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]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]dno
Use index doublets (vectors) for correlation function instead of
triplets (planes)
-[no]averyes
Average over molecules
-acflen int -1
Length of the ACF, default is half the number of frames
-[no]normalizeyes
Normalize ACF
-P enum 0
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
3
-fitfn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
exp9
-ncskip int 0
Skip N points in the output file of correlation functions
-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 till the end
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_rotacf(1)