| VERSION 3.3_beta_20050823 |
g_sorient analyzes solvent orientation around solutes.
It calculates two angles between the vector from one or more
reference positions to the first atom of each solvent molecule:
theta1: the angle with the vector from the first atom of the solvent
molecule to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the
same three atoms.
The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
consist of 3 atoms per solvent molecule.
Only solvent molecules between -rmin and -rmax are
considered for -o and -no each frame.
-o: distribtion of cos(theta1) for rmin<=r<=rmax.
-no: distribution of 3cos^2(theta2)-1 for rmin<=r<=rmax.
-ro: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the distance.
-co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos^2(theta2)-1 as a function of r.
| 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 |
| -n | index.ndx | Input, Opt. | Index file |
| -o | sori.xvg | Output | xvgr/xmgr file |
| -no | snor.xvg | Output | xvgr/xmgr file |
| -ro | sord.xvg | Output | xvgr/xmgr file |
| -co | scum.xvg | Output | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help 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 |
| -[no]xvgr | bool | yes | Add specific codes (legends etc.) in the output xvg files for the xmgrace program |
| -[no]com | bool | no | Use the center of mass as the reference postion |
| -rmin | real | 0 | Minimum distance |
| -rmax | real | 0.5 | Maximum distance |
| -bin | real | 0.02 | Binwidth |
| -[no]pbc | bool | no | Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. |