g_spol_d (1) - Linux Manuals

g_spol_d: analyzes solvent dipole orientation and polarization around solutes

NAME

g_spol - analyzes solvent dipole orientation and polarization around solutes

VERSION 4.0.1

SYNOPSIS

g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -refat int -rmin real -rmax real -dip real -bw real

DESCRIPTION

g_spol analyzes dipoles around a solute; it is especially useful for polarizable water. A group of reference atoms, or a center of mass reference (option -com) and a group of solvent atoms is required. The program splits the group of solvent atoms into molecules. For each solvent molecule the distance to the closest atom in reference group or to the COM is determined. A cumulative distribution of these distances is plotted. For each distance between -rmin and -rmax the inner product of the distance vector and the dipole of the solvent molecule is determined. The average of these dipole components is printed. The same is done for the polarization, where the average dipole is subtracted from the instantaneous dipole. The magnitude of the average dipole is set with the option -dip, the direction is defined by the vector from the first atom in the selected solvent group to the midpoint between the second and the third atom.

FILES

-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-s topol.tpr Input
 Run input file: tpr tpb tpa 

-n index.ndx Input, Opt.
 Index file 

-o scdist.xvg Output
 xvgr/xmgr file 

OTHER OPTIONS

-[no]hno
 Print 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]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]comno
 Use the center of mass as the reference postion

-refat int 1
 The reference atom of the solvent molecule

-rmin real 0
 Maximum distance (nm)

-rmax real 0.32
 Maximum distance (nm)

-dip real 0
 The average dipole (D)

-bw real 0.01
 The bin width