Analyze solvent orientation around solutes
gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
[-co [<.xvg>]] [-rc [<.xvg>]] [-nice <int>] [-b <time>]
[-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
[-[no]com] [-[no]v23] [-rmin <real>] [-rmax <real>]
[-cbin <real>] [-rbin <real>] [-[no]pbc]
gmx 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:
theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta_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(theta_1) for rmin=r=rmax.
-no: distribution of cos(theta_2) for rmin=r=rmax.
-ro: cos(theta_1) and 3cos(2theta_2)-1 as a function of the distance.
-co: the sum over all solvent molecules within distance r of cos(theta_1) and 3cos(2(theta_2)-1) as a function of r.
-rc: the distribution of the solvent molecules as a function of r
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (sori.xvg) (Output)
xvgr/xmgr file
-no [<.xvg>] (snor.xvg) (Output)
xvgr/xmgr file
-ro [<.xvg>] (sord.xvg) (Output)
xvgr/xmgr file
-co [<.xvg>] (scum.xvg) (Output)
xvgr/xmgr file
-rc [<.xvg>] (scount.xvg) (Output)
xvgr/xmgr file
Other options:
-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 (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]com (no)
Use the center of mass as the reference postion
-[no]v23 (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 (no)
Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
More information about GROMACS is available at <http://www.gromacs.org/>.