gmx-sorient - Man Page

gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
            [-co [<.xvg>]] [-rc [<.xvg>]] [-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: distribution 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 files:

-f [<.xtc/.trr/...>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/...>] (topol.tpr)

Structure+mass(db): tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-o [<.xvg>] (sori.xvg)

xvgr/xmgr file

-no [<.xvg>] (snor.xvg)

xvgr/xmgr file

-ro [<.xvg>] (sord.xvg)

xvgr/xmgr file

-co [<.xvg>] (scum.xvg)

xvgr/xmgr file

-rc [<.xvg>] (scount.xvg)

xvgr/xmgr file

Other options:

-b <time> (0)

Time of first frame to read from trajectory (default unit ps)

-e <time> (0)

Time of last frame to read from trajectory (default unit ps)

-dt <time> (0)

Only use frame when t MOD dt = first time (default unit 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 position

-[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.

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

2024, GROMACS development team

gmx(1).