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g_gyrateMain Table of Contents |
VERSION 3.2.0
Sun 25 Jan 2004
| VERSION 3.2.0 |
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.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Generic trajectory: xtc trr trj gro g96 pdb |
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb xml |
| -o | gyrate.xvg | Output | xvgr/xmgr file |
| -acf | moi-acf.xvg | Output, Opt. | xvgr/xmgr file |
| -n | index.ndx | Input, Opt. | Index file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -[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). |
| -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 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 till the end |