.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_density - calculates the density of the system

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_density\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-ei" " electrons.dat "
.BI "\-o" " density.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-d" " string "
.BI "\-sl" " int "
.BI "\-dens" " enum "
.BI "\-ng" " int "
.BI "\-[no]symm" ""
.BI "\-[no]center" ""
.SH DESCRIPTION
\&Compute partial densities across the box, using an index file.


\&For the total density of NPT simulations, use \fB g_energy\fR instead.
\&


\&Densities are in kg/m3, and number densities or electron densities can also be
\&calculated. For electron densities, a file describing the number of
\&electrons for each type of atom should be provided using \fB \-ei\fR.
\&It should look like:

\&   \fB 2\fR

\&   \fB atomname = nrelectrons\fR

\&   \fB atomname = nrelectrons\fR

\&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.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-ei" " electrons.dat" 
.B Input, Opt.
 Generic data file 

.BI "\-o" " density.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-d"  " string" " Z" 
 Take the normal on the membrane in direction X, Y or Z.

.BI "\-sl"  " int" " 50" 
 Divide the box in nr slices.

.BI "\-dens"  " enum" " mass" 
 Density: \fB mass\fR, \fB number\fR, \fB charge\fR or \fB electron\fR

.BI "\-ng"  " int" " 1" 
 Number of groups to compute densities of

.BI "\-[no]symm"  "no    "
 Symmetrize the density along the axis, with respect to the center. Useful for bilayers.

.BI "\-[no]center"  "no    "
 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.

.SH KNOWN PROBLEMS
\- When calculating electron densities, atomnames are used instead of types. This is bad.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.