xenial (1) gmx-density.1.gz

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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] [-[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 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.
       Option -relative performs the binning in relative instead of absolute box  coordinates,  and  scales  the
       final  output  with the average box dimension along the output axis. This can be used in combination with
       -center.

       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.

       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 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)
              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>
              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 ALSO
       gmx(1)

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


       2015, GROMACS development team