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Man Pages


Manual Reference Pages  -  GMX-SORIENT (1)

NAME

gmx-sorient - Analyze solvent orientation around solutes

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

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]

DESCRIPTION

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

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.

SEE ALSO

gromacs(7)

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

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VERSION 5.0.6 GMX-SORIENT (1)

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