g_rotacf(1)

NAME
g_rotacf VERSION 3.2.0

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]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
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Generic run input: tpr tpb tpa xml -n index.ndx Input
 Index file -o rotacf.xvg Output
 xvgr/xmgr file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -[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 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