Ubuntu Manpage: gmx-density - Calculate the density of the system

Provided by: gromacs-data_2024.2-1_all

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 profiles 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 automatically 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 various groups across a lipid
bilayer, typically with the z axis being the normal 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 bilayer centered in the box will move a bit up/down due
to these fluctuations, 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 center 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 exhibit undulatory fluctuations,
where there are 'waves' forming in the system. 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

       -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.

COPYRIGHT