| VERSION 4.6.5 |
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:
θ_1: the angle with the vector from the first atom of the solvent
molecule to the midpoint between atoms 2 and 3.
θ_2: the angle with the normal of the solvent plane, defined by the
same three atoms, or, when the option -v23 is set,
the angle with the vector between atoms 2 and 3.
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(θ_1) for rmin<=r<=rmax.
-no: distribution of cos(θ_2) for rmin<=r<=rmax.
-ro:
-co: the sum over all solvent molecules within distance r of cos(θ_1) and 3cos(^2(θ_2)-1) as a function of r.
-rc: the distribution of the solvent molecules as a function of r
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 | 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 |
-rc | scount.xvg | Output | xvgr/xmgr file |
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 |
-[no]com | bool | no | Use the center of mass as the reference postion |
-[no]v23 | bool | no | Use the vector between atoms 2 and 3 |
-rmin | real | 0 | Minimum distance (nm) |
-rmax | real | 0.5 | Maximum distance (nm) |
-cbin | real | 0.02 | Binwidth for the cosine |
-rbin | real | 0.02 | Binwidth for r (nm) |
-[no]pbc | bool | no | Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. |