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

6       g_gyrate - calculates the radius of gyration
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8       VERSION 4.5
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SYNOPSIS

11       g_gyrate  -f  traj.xtc  -s  topol.tpr  -n  index.ndx -o gyrate.xvg -acf
12       moi-acf.xvg -[no]h -[no]version -nice int -b  time  -e  time  -dt  time
13       -[no]w  -xvg  enum -nmol int -[no]q -[no]p -[no]moi -nz int -acflen int
14       -[no]normalize -P enum -fitfn enum -ncskip int -beginfit  real  -endfit
15       real
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DESCRIPTION

18       g_gyrate  computes  the  radius of gyration of a group of atoms and the
19       radii of gyration about the x, y and z axes, as a function of time. The
20       atoms are explicitly mass weighted.
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23       With  the   -nmol  option the radius of gyration will be calculated for
24       multiple molecules by splitting the analysis  group  in  equally  sized
25       parts.
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28       With  the  option   -nz 2D radii of gyration in the x-y plane of slices
29       along the z-axis are calculated.
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FILES

32       -f traj.xtc Input
33        Trajectory: xtc trr trj gro g96 pdb cpt
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35       -s topol.tpr Input
36        Structure+mass(db): tpr tpb tpa gro g96 pdb
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38       -n index.ndx Input, Opt.
39        Index file
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41       -o gyrate.xvg Output
42        xvgr/xmgr file
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44       -acf moi-acf.xvg Output, Opt.
45        xvgr/xmgr file
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OTHER OPTIONS

49       -[no]hno
50        Print help info and quit
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52       -[no]versionno
53        Print version info and quit
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55       -nice int 19
56        Set the nicelevel
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58       -b time 0
59        First frame (ps) to read from trajectory
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61       -e time 0
62        Last frame (ps) to read from trajectory
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64       -dt time 0
65        Only use frame when t MOD dt = first time (ps)
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67       -[no]wno
68        View output xvg, xpm, eps and pdb files
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70       -xvg enum xmgrace
71        xvg plot formatting:  xmgrace,  xmgr or  none
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73       -nmol int 1
74        The number of molecules to analyze
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76       -[no]qno
77        Use absolute value of the  charge  of  an  atom  as  weighting  factor
78       instead of mass
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80       -[no]pno
81        Calculate the radii of gyration about the principal axes.
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83       -[no]moino
84        Calculate the moments of inertia (defined by the principal axes).
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86       -nz int 0
87        Calculate the 2D radii of gyration of  slices along the z-axis
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89       -acflen int -1
90        Length of the ACF, default is half the number of frames
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92       -[no]normalizeyes
93        Normalize ACF
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95       -P enum 0
96        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
97       3
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99       -fitfn enum none
100        Fit function:  none,  exp,  aexp,   exp_exp,   vac,   exp5,   exp7  or
101       exp9
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103       -ncskip int 0
104        Skip N points in the output file of correlation functions
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106       -beginfit real 0
107        Time where to begin the exponential fit of the correlation function
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109       -endfit real -1
110        Time  where to end the exponential fit of the correlation function, -1
111       is until the end
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SEE ALSO

115       gromacs(7)
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117       More  information  about  GROMACS  is  available  at   <http://www.gro‐
118       macs.org/>.
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122                                Thu 26 Aug 2010                    g_gyrate(1)
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