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g_sorientMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
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:
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, 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(theta1) for rmin<=r<=rmax.
-no: distribution of cos(theta2) 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.
-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 | 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]com | gmx_bool | no | Use the center of mass as the reference postion |
| -[no]v23 | gmx_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 | gmx_bool | no | Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. |