## g_gyrate

Main Table of Contents

VERSION 4.6
Sat 19 Jan 2013

### Description

`g_gyrate` computes the radius of gyration of a group of atoms and the radii of gyration about the <it>x</it>-, <it>y</it>- and <it>z</it>-axes, as a function of time. The atoms are explicitly mass weighted.

With the `-nmol` option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts.

With the option `-nz` 2D radii of gyration in the <it>x-y</it> plane of slices along the <it>z</it>-axis are calculated.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-s` | `topol.tpr` | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-o` | `gyrate.xvg` | Output | xvgr/xmgr file
`-acf` | `moi-acf.xvg` | Output, Opt. | xvgr/xmgr file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | bool | `no` | Print help info and quit
`-[no]version` | bool | `no` | Print version 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` | bool | `no` | View output `.xvg`, `.xpm`, `.eps` and `.pdb` files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-nmol` | int | `1` | The number of molecules to analyze
`-[no]q` | bool | `no` | Use absolute value of the charge of an atom as weighting factor instead of mass
`-[no]p` | bool | `no` | Calculate the radii of gyration about the principal axes.
`-[no]moi` | bool | `no` | Calculate the moments of inertia (defined by the principal axes).
`-nz` | int | `0` | Calculate the 2D radii of gyration of this number of slices along the z-axis
`-acflen` | int | `-1` | Length of the ACF, default is half the number of frames
`-[no]normalize` | bool | `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`, `exp9` or `erffit`
`-ncskip` | int | `0` | Skip this many 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 until the end

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