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g_sorient
Langue: en
Version: 111398 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
g_sorient VERSION 3.3_beta_20050823SYNOPSIS
g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -rmin real -rmax real -bin real -[no]pbcDESCRIPTION
g_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: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.theta2: the angle with the normal of the solvent plane, defined by the same three atoms.
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(theta1) for rmin=r=rmax.
-no : distribution of 3cos2(theta2)-1 for rmin=r=rmax.
-ro : cos(theta1) and 3cos2(theta2)-1 as a function of the distance.
-co : the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r.
FILES
-f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt.
Index file
-o sori.xvg Output
xvgr/xmgr file
-no snor.xvg Output
xvgr/xmgr file
-ro sord.xvg Output
xvgr/xmgr file
-co scum.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]h noPrint help info and quit
-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
-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[no]com no
Use the center of mass as the reference postion
-rmin real 0
Minimum distance
-rmax real 0.5
Maximum distance
-bin real 0.02
Binwidth
-[no]pbc no
Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre