gmx-density(1) GROMACS Manual gmx-density(1)NAMEgmx-density - Calculate the density of the system
SYNOPSIS
gmx density [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-s [<.tpr/.tpb/...>]] [-ei [<.dat>]] [-o [<.xvg>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-xvg <enum>] [-d <string>] [-sl <int>]
[-dens <enum>] [-ng <int>] [-[no]center] [-[no]symm]
[-[no]relative]
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 behav‐
iour 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 auto‐
matically turn on -center too. Option -relative performs the binning in
relative instead of absolute box coordinates, and scales the final out‐
put with the average box dimension along the output axis. This can be
used in combination with -center.
Densities are in kg/m3, and number densities or electron densities can
also be calculated. For electron densities, a file describing the num‐
ber 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 sys‐
tem. Since Gromacs places the box between the origin and positive coor‐
dinates, 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 pro‐
file. 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.
Even the centered calculation will lead to some smearing out the output
profiles, as lipids themselves are compressed and expanded. In most
cases you probably want this (since it corresponds to macroscopic
experiments), but if you want to look at molecular details you can use
the -relative option to attempt to remove even more of the effects of
volume fluctuations.
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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-ei [<.dat>] (electrons.dat) (Input, Optional)
Generic data file
-o [<.xvg>] (density.xvg) (Output)
xvgr/xmgr file
Other options:
-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]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.
-[no]relative (no)
Use relative coordinates for changing boxes and scale output by
average dimensions.
KNOWN ISSUES
- When calculating electron densities, atomnames are used instead of
types. This is bad.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-density(1)
