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g_density
Langue: en
Version: 369384 (fedora - 01/12/10)
Section: 1 (Commandes utilisateur)
NAME
g_density - calculates the density of the systemVERSION 4.5
SYNOPSIS
g_density -f traj.xtc -n index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d string -sl int -dens enum -ng int -[no]symm -[no]centerDESCRIPTION
Compute partial densities across the box, using an index file. Densities in kg/m3, number densities or electron densities can be calculated. For electron densities, a file describing the number of electrons for each type of atom should be provided using -ei. It should look like:2
atomname = nrelectrons
atomname = nrelectrons
The first line contains the number of lines to read from the file. There should be one line for each unique atom name in your system. The number of electrons for each atom is modified by its atomic partial charge.
FILES
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input, Opt.
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-ei electrons.dat Input, Opt.
Generic data file
-o density.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hnoPrint help info and quit
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-d string Z
Take the normal on the membrane in direction X, Y or Z.
-sl int 50
Divide the box in nr slices.
-dens enum mass
Density: mass, number, charge or electron
-ng int 1
Number of groups to compute densities of
-[no]symmno
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-[no]centerno
Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0.
KNOWN PROBLEMS
- When calculating electron densities, atomnames are used instead of types. This is bad.SEE ALSO
gromacs(7)More information about GROMACS is available at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre