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GMX-SORIENT(1) GROMACS GMX-SORIENT(1) 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 sol- vent 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 an- gle 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 consid- ered 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 dis- tance. -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. SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-SORIENT(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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