gmx sorient¶
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)- 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.