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g_gyrateMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_gyrate computes the radius of gyration of a group of atoms and the radii of gyration about the x, y and z 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 x-y plane of slices along the z-axis are calculated.
| 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 |
| option | type | default | description |
|---|---|---|---|
| -[no]h | gmx_bool | no | Print help info and quit |
| -[no]version | gmx_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 | gmx_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 | gmx_bool | no | Use absolute value of the charge of an atom as weighting factor instead of mass |
| -[no]p | gmx_bool | no | Calculate the radii of gyration about the principal axes. |
| -[no]moi | gmx_bool | no | Calculate the moments of inertia (defined by the principal axes). |
| -nz | int | 0 | Calculate the 2D radii of gyration of # slices along the z-axis |
| -acflen | int | -1 | Length of the ACF, default is half the number of frames |
| -[no]normalize | gmx_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 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 until the end |