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] [-[no]relative]
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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.  Option -relative performs the binning
31       in relative instead of absolute box coordinates, and scales  the  final
32       output  with  the average box dimension along the output axis. This can
33       be used in combination with -center.
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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.
48
49       IMPORTANT CONSIDERATIONS FOR BILAYERS
50
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
55       bilayers can be complicated.  The first problem that  while  both  pro‐
56       teins  and  lipids  have  low volume compressibility, lipids have quite
57       high area compressiblity. This means the shape of  the  box  (thickness
58       and  area/lipid)  will fluctuate substantially even for a fully relaxed
59       system. Since GROMACS places the box between the  origin  and  positive
60       coordinates, 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.
68
69       Even the centered calculation will lead to some smearing out the output
70       profiles,  as  lipids  themselves  are compressed and expanded. In most
71       cases you probably want  this  (since  it  corresponds  to  macroscopic
72       experiments),  but if you want to look at molecular details you can use
73       the -relative option to attempt to remove even more of the  effects  of
74       volume fluctuations.
75
76       Finally,  large bilayers that are not subject to a surface tension will
77       exhibit undulatory fluctuations, where there are ‘waves’ forming in the
78       system.   This  is a fundamental property of the biological system, and
79       if you are comparing against experiments you likely want to include the
80       undulation smearing effect.
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OPTIONS

83       Options to specify input files:
84
85       -f [<.xtc/.trr/…>] (traj.xtc)
86              Trajectory: xtc trr cpt gro g96 pdb tng
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88       -n [<.ndx>] (index.ndx) (Optional)
89              Index file
90
91       -s [<.tpr>] (topol.tpr)
92              Portable xdr run input file
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94       -ei [<.dat>] (electrons.dat) (Optional)
95              Generic data file
96
97       Options to specify output files:
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99       -o [<.xvg>] (density.xvg)
100              xvgr/xmgr file
101
102       Other options:
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104       -b <time> (0)
105              Time of first frame to read from trajectory (default unit ps)
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107       -e <time> (0)
108              Time of last frame to read from trajectory (default unit ps)
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110       -dt <time> (0)
111              Only use frame when t MOD dt = first time (default unit ps)
112
113       -[no]w (no)
114              View output .xvg, .xpm, .eps and .pdb files
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116       -xvg <enum> (xmgrace)
117              xvg plot formatting: xmgrace, xmgr, none
118
119       -d <string> (Z)
120              Take the normal on the membrane in direction X, Y or Z.
121
122       -sl <int> (50)
123              Divide the box in this number of slices.
124
125       -dens <enum> (mass)
126              Density: mass, number, charge, electron
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128       -ng <int> (1)
129              Number of groups of which to compute densities.
130
131       -[no]center (no)
132              Perform  the  binning  relative  to the center of the (changing)
133              box. Useful for bilayers.
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135       -[no]symm (no)
136              Symmetrize the density along the axis, with respect to the  cen‐
137              ter. Useful for bilayers.
138
139       -[no]relative (no)
140              Use  relative coordinates for changing boxes and scale output by
141              average dimensions.
142

KNOWN ISSUES

144       · When calculating electron densities, atomnames are  used  instead  of
145         types. This is bad.
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SEE ALSO

148       gmx(1)
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150       More     information    about    GROMACS    is    available    at    <‐
151       http://www.gromacs.org/>.
152
154       2019, GROMACS development team
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1592018.7                           May 29, 2019                   GMX-DENSITY(1)
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