This is the command gmx-sorient that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-sorient - Analyze solvent orientation around solutes
SYNOPSIS
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]
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: 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
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)
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>
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.
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