NAME¶

g_rotacf - calculates the rotational correlation function for molecules VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[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 until 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 -[no]versionno
Print version 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 -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -[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, exp9 or erffit -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 until the end

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.