1GMX-DENSITY(1)                      GROMACS                     GMX-DENSITY(1)
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NAME

6       gmx-density - Calculate the density of the system
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SYNOPSIS

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

16       gmx  density  computes partial densities across the box, using an index
17       file.
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19       For the total density of NPT simulations, use gmx energy instead.
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21       Option -center performs the histogram binning relative to the center of
22       an arbitrary group, in absolute box coordinates. If you are calculating
23       profiles along the Z axis box dimension bZ, output would be from  -bZ/2
24       to  bZ/2  if you center based on the entire system.  Note that this be‐
25       haviour has changed in GROMACS 5.0; earlier versions merely performed a
26       static  binning  in  (0,bZ)  and shifted the output. Now we compute the
27       center for each frame and bin in (-bZ/2,bZ/2).
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29       Option -symm symmetrizes the output around the center. This will  auto‐
30       matically  turn on -center too.  The binning is now always performed in
31       relative coordinates to account for changing box dimensions with  pres‐
32       sure  coupling,  with  the  output  scaled to the average box dimension
33       along the output axis.
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35       Densities are in kg/m^3, and number densities or electron densities can
36       also  be calculated. For electron densities, a file describing the num‐
37       ber of electrons for each type of atom should be  provided  using  -ei.
38       It should look like:
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40          2
41          atomname = nrelectrons
42          atomname = nrelectrons
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44       The  first  line  contains  the  number of lines to read from the file.
45       There should be one line for each unique atom name in your system.  The
46       number  of  electrons  for  each atom is modified by its atomic partial
47       charge.
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49       IMPORTANT CONSIDERATIONS FOR BILAYERS
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51       One of the most common usage scenarios is to calculate the  density  of
52       various  groups across a lipid bilayer, typically with the z axis being
53       the normal direction. For short simulations, small systems,  and  fixed
54       box  sizes this will work fine, but for the more general case lipid bi‐
55       layers can be complicated.  The first problem that while both  proteins
56       and lipids have low volume compressibility, lipids have quite high area
57       compressiblity.  This  means  the  shape  of  the  box  (thickness  and
58       area/lipid)  will fluctuate substantially even for a fully relaxed sys‐
59       tem. Since GROMACS places the box between the origin and positive coor‐
60       dinates,  this  in  turn  means that a bilayer centered in the box will
61       move a bit up/down due to these fluctuations, and smear out  your  pro‐
62       file. The easiest way to fix this (if you want pressure coupling) is to
63       use the -center option that calculates the density profile with respect
64       to the center of the box. Note that you can still center on the bilayer
65       part even if you have a complex non-symmetric  system  with  a  bilayer
66       and,  say,  membrane  proteins  - then our output will simply have more
67       values on one side of the (center) origin reference.
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69       Finally, large bilayers that are not subject to a surface tension  will
70       exhibit undulatory fluctuations, where there are 'waves' forming in the
71       system.  This is a fundamental property of the biological  system,  and
72       if you are comparing against experiments you likely want to include the
73       undulation smearing effect.
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OPTIONS

76       Options to specify input files:
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78       -f [<.xtc/.trr/...>] (traj.xtc)
79              Trajectory: xtc trr cpt gro g96 pdb tng
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81       -n [<.ndx>] (index.ndx) (Optional)
82              Index file
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84       -s [<.tpr>] (topol.tpr)
85              Portable xdr run input file
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87       -ei [<.dat>] (electrons.dat) (Optional)
88              Generic data file
89
90       Options to specify output files:
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92       -o [<.xvg>] (density.xvg)
93              xvgr/xmgr file
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95       Other options:
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97       -b <time> (0)
98              Time of first frame to read from trajectory (default unit ps)
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100       -e <time> (0)
101              Time of last frame to read from trajectory (default unit ps)
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103       -dt <time> (0)
104              Only use frame when t MOD dt = first time (default unit ps)
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106       -[no]w (no)
107              View output .xvg, .xpm, .eps and .pdb files
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109       -xvg <enum> (xmgrace)
110              xvg plot formatting: xmgrace, xmgr, none
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112       -d <string> (Z)
113              Take the normal on the membrane in direction X, Y or Z.
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115       -sl <int> (50)
116              Divide the box in this number of slices.
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118       -dens <enum> (mass)
119              Density: mass, number, charge, electron
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121       -ng <int> (1)
122              Number of groups of which to compute densities.
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124       -[no]center (no)
125              Perform the binning relative to the  center  of  the  (changing)
126              box. Useful for bilayers.
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128       -[no]symm (no)
129              Symmetrize  the density along the axis, with respect to the cen‐
130              ter. Useful for bilayers.
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KNOWN ISSUES

133       • When calculating electron densities, atomnames are  used  instead  of
134         types. This is bad.
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SEE ALSO

137       gmx(1)
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139       More     information    about    GROMACS    is    available    at    <‐
140       http://www.gromacs.org/>.
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143       2022, GROMACS development team
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1482022.3                           Sep 02, 2022                   GMX-DENSITY(1)
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