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g_rotacfMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_rotacf calculates the rotational correlation function for molecules. Three atoms (i,j,k) must be given in the index file, defining two vectors ij and jk. The rotational acf is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of the two vectors. Since three atoms span a plane, the order of the three atoms does not matter. Optionally, controlled by the -d switch, you can calculate the rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file.
EXAMPLES
g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0
This will calculate the rotational correlation function using a first order Legendre polynomial of the angle of a vector defined by the index file. The correlation function will be fitted from 2.5 ps till 20.0 ps to a two parameter exponential.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -s | topol.tpr | Input | Run input file: tpr tpb tpa |
| -n | index.ndx | Input | Index file |
| -o | rotacf.xvg | Output | 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 |
| -[no]d | gmx_bool | no | Use index doublets (vectors) for correlation function instead of triplets (planes) |
| -[no]aver | gmx_bool | yes | Average over molecules |
| -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 |