.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rotacf - calculates the rotational correlation function for molecules

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " rotacf.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]d" ""
.BI "\-[no]aver" ""
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&\fB g_rotacf\fR 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 \fB \-d\fR switch, you can
\&calculate the rotational correlation function for linear molecules
\&by specifying two atoms (i,j) in the index file.
\&


\&EXAMPLES


\&\fB g_rotacf \-P 1 \-nparm 2 \-fft \-n index \-o rotacf\-x\-P1
\&\-fa expfit\-x\-P1 \-beginfit 2.5 \-endfit 20.0\fR


\&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.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-o" " rotacf.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]d"  "no    "
 Use index doublets (vectors) for correlation function instead of triplets (planes)

.BI "\-[no]aver"  "yes   "
 Average over molecules

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.