Man Linux: Main Page and Category List

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)