man g_densmap (Commandes) - g_densmap VERSION 3.3_beta_20050823
NAME
g_densmap VERSION 3.3_beta_20050823
SYNOPSIS
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -o densmap.xpm -[no]h -nice int -b time -e time -dt time -[no]w -bin real -nx int -nz int -amax real -rmax real -[no]mirror -dmax real
DESCRIPTION
g_densmap computes 2D number-density maps. It can make planar and axial-radial density maps. The output .xpm file can be visualized with for instance xv and can be converted to postscript with xpm2ps.
The default analysis is a 2-D number-density map for a selected group of atoms in the x-z plane. The grid spacing is set with the option
-bin -nx or -nz is non-zero, the grid size is set by this option. Box size fluctuations are properly taken into account.
When options -amax and -rmax are set, an axial-radial number-density map is made. Three groups should be supplied, the centers of mass of the first two groups define the axis, the third defines the analysis group. The axial direction goes from -amax to +amax, where the center is defined as the midpoint between the centers of mass and the positive direction goes from the first to the second center of mass. The radial direction goes from 0 to rmax or from -rmax to +rmax when the -mirror option has been set.
When you do not want the scale in the output to go from zero to the maximum density, you can set the maximum with the option -dmax
FILES
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt. Index file
-o densmap.xpm Output X PixMap compatible matrix file
OTHER OPTIONS
-[no]h no 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]w no View output xvg, xpm, eps and pdb files
-bin real 0.02 Grid size
-nx int 0 Number of grid cells in x direction
-nz int 0 Number of grid cells in z direction
-amax real 0 Maximum axial distance from the center
-rmax real 0 Maximum radial distance
-[no]mirror no Add the mirror image below the axial axis
-dmax real 0 Maximum density (0 means calculate it)