g_rotacf VERSION 3.3_beta_20050823

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

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

-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

-[no]h no 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]w no View output xvg, xpm, eps and pdb files

-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.