1g_rotacf(1)               GROMACS suite, VERSION 4.5               g_rotacf(1)
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NAME

6       g_rotacf - calculates the rotational correlation function for molecules
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8       VERSION 4.5
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SYNOPSIS

11       g_rotacf  -f  traj.xtc  -s  topol.tpr -n index.ndx -o rotacf.xvg -[no]h
12       -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]d
13       -[no]aver  -acflen  int  -[no]normalize -P enum -fitfn enum -ncskip int
14       -beginfit real -endfit real
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DESCRIPTION

17       g_rotacf calculates the rotational correlation function for  molecules.
18       Three  atoms (i,j,k) must be given in the index file, defining two vec‐
19       tors ij and jk. The rotational acf is calculated as the autocorrelation
20       function  of  the vector n = ij x jk, i.e. the cross product of the two
21       vectors.  Since three atoms span a plane, the order of the three  atoms
22       does  not matter. Optionally, controlled by the -d switch, you can cal‐
23       culate the rotational correlation  function  for  linear  molecules  by
24       specifying two atoms (i,j) in the index file.
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26
27       EXAMPLES
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30       g_rotacf  -P  1  -nparm  2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
31       -beginfit 2.5 -endfit 20.0
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34       This will calculate the rotational correlation function using  a  first
35       order Legendre polynomial of the angle of a vector defined by the index
36       file. The correlation function will be fitted from 2.5 ps till 20.0  ps
37       to a two parameter exponential.
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FILES

40       -f traj.xtc Input
41        Trajectory: xtc trr trj gro g96 pdb cpt
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43       -s topol.tpr Input
44        Run input file: tpr tpb tpa
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46       -n index.ndx Input
47        Index file
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49       -o rotacf.xvg Output
50        xvgr/xmgr file
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OTHER OPTIONS

54       -[no]hno
55        Print help info and quit
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57       -[no]versionno
58        Print version info and quit
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60       -nice int 19
61        Set the nicelevel
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63       -b time 0
64        First frame (ps) to read from trajectory
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66       -e time 0
67        Last frame (ps) to read from trajectory
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69       -dt time 0
70        Only use frame when t MOD dt = first time (ps)
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72       -[no]wno
73        View output xvg, xpm, eps and pdb files
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75       -xvg enum xmgrace
76        xvg plot formatting:  xmgrace,  xmgr or  none
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78       -[no]dno
79        Use  index  doublets  (vectors)  for  correlation  function instead of
80       triplets (planes)
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82       -[no]averyes
83        Average over molecules
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85       -acflen int -1
86        Length of the ACF, default is half the number of frames
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88       -[no]normalizeyes
89        Normalize ACF
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91       -P enum 0
92        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
93       3
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95       -fitfn enum none
96        Fit  function:   none,   exp,   aexp,   exp_exp,  vac,  exp5,  exp7 or
97       exp9
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99       -ncskip int 0
100        Skip N points in the output file of correlation functions
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102       -beginfit real 0
103        Time where to begin the exponential fit of the correlation function
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105       -endfit real -1
106        Time where to end the exponential fit of the correlation function,  -1
107       is until the end
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SEE ALSO

111       gromacs(7)
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113       More   information  about  GROMACS  is  available  at  <http://www.gro‐
114       macs.org/>.
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118                                Thu 26 Aug 2010                    g_rotacf(1)
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