Provided by: gromacs-data_2019.3-2_all bug

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)
              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.

       -[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/>.

COPYRIGHT

       2019, GROMACS development team