table of contents
g_densmap(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_densmap(1) |
NAME¶
g_densmap - calculates 2D planar or axial-radial density mapsSYNOPSIS¶
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -od densmap.dat -o densmap.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -bin real -aver enum -xmin real -xmax real -n1 int -n2 int -amax real -rmax real -[no]mirror -[no]sums -unit enum -dmin real -dmax realDESCRIPTION¶
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. Optionally, output can be in text form to a .dat file with -od, instead of the usual .xpm file with -o.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
Generic data file
X PixMap compatible matrix file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
Grid size (nm)
The direction to average over: z, y or x
Minimum coordinate for averaging
Maximum coordinate for averaging
Number of grid cells in the first direction
Number of grid cells in the second direction
Maximum axial distance from the center
Maximum radial distance
Add the mirror image below the axial axis
Print density sums (1D map) to stdout
Unit for the output: nm-3, nm-2 or count
Minimum density in output
Maximum density in output (0 means calculate it)
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |