home | help 
GMX-DENSITY(1)			     GROMACS			  GMX-DENSITY(1)

NAME
     gmx-density - Calculate the density of the system

SYNOPSIS
	gmx density [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
		    [-ei [<.dat>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
		    [-dt <time>] [-[no]w] [-xvg <enum>] [-d <string>]
		    [-sl <int>] [-dens <enum>] [-ng <int>] [-[no]center]
		    [-[no]symm]

DESCRIPTION
     gmx density computes partial densities across the box, using an index file.

     For the total density of NPT simulations, use gmx energy instead.

     Option  -center performs the histogram binning relative to the center of an
     arbitrary group, in absolute box coordinates. If you are  calculating  pro-
     files along the Z axis box dimension bZ, output would be from -bZ/2 to bZ/2
     if  you  center  based  on the entire system.  Note that this behaviour has
     changed in GROMACS 5.0; earlier versions merely performed a static  binning
     in  (0,bZ) and shifted the output. Now we compute the center for each frame
     and bin in (-bZ/2,bZ/2).

     Option -symm symmetrizes the output around the center. This will  automati-
     cally turn on -center too.  The binning is now always performed in relative
     coordinates  to account for changing box dimensions with pressure coupling,
     with the output scaled to the average box dimension along the output axis.

     Densities are in kg/m^3, 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 -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.

     IMPORTANT CONSIDERATIONS FOR BILAYERS

     One of the most common usage scenarios is to calculate the density of vari-
     ous groups across a lipid bilayer, typically with the z axis being the nor-
     mal  direction.  For  short simulations, small systems, and fixed box sizes
     this will work fine, but for the more general case lipid  bilayers  can  be
     complicated.   The  first	problem that while both proteins and lipids have
     low volume compressibility, lipids have  quite  high  area  compressiblity.
     This  means  the shape of the box (thickness and area/lipid) will fluctuate
     substantially even for a fully relaxed system. Since GROMACS places the box
     between the origin and positive coordinates, this in turn means that a  bi-
     layer  centered  in  the  box will move a bit up/down due to these fluctua-
     tions, and smear out your profile. The easiest way to fix this (if you want
     pressure coupling) is to use the -center option that calculates the density
     profile with respect to the center of the box. Note that you can still cen-
     ter on the bilayer part even if you have  a  complex  non-symmetric  system
     with  a  bilayer  and, say, membrane proteins - then our output will simply
     have more values on one side of the (center) origin reference.

     Finally, large bilayers that are not subject to a surface tension will  ex-
     hibit  undulatory fluctuations, where there are 'waves' forming in the sys-
     tem.  This is a fundamental property of the biological system, and  if  you
     are comparing against experiments you likely want to include the undulation
     smearing effect.

OPTIONS
     Options to specify input files:

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -n [<.ndx>] (index.ndx) (Optional)
	    Index file

     -s [<.tpr>] (topol.tpr)
	    Portable xdr run input file

     -ei [<.dat>] (electrons.dat) (Optional)
	    Generic data file

     Options to specify output files:

     -o [<.xvg>] (density.xvg)
	    xvgr/xmgr file

     Other options:

     -b <time> (0)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit ps)

     -[no]w (no)
	    View output .xvg, .xpm, .eps and .pdb files

     -xvg <enum> (xmgrace)
	    xvg plot formatting: xmgrace, xmgr, none

     -d <string> (Z)
	    Take the normal on the membrane in direction X, Y or Z.

     -sl <int> (50)
	    Divide the box in this number of slices.

     -dens <enum> (mass)
	    Density: mass, number, charge, electron

     -ng <int> (1)
	    Number of groups of which to compute densities.

     -[no]center (no)
	    Perform  the  binning  relative to the center of the (changing) box.
	    Useful for bilayers.

     -[no]symm (no)
	    Symmetrize the density along the axis, with respect to  the  center.
	    Useful for bilayers.

KNOWN ISSUES
     * When calculating electron densities, atomnames are used instead of types.
       This is bad.

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			  GMX-DENSITY(1)
home | help