1GMX-DENSITY(1) GROMACS GMX-DENSITY(1)
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6 gmx-density - Calculate the density of the system
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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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16 gmx density computes partial densities across the box, using an index
17 file.
18 For the total density of NPT simulations, use gmx energy instead.
20 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).
28 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.
34 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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41 atomname = nrelectrons
42 atomname = nrelectrons
43 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 IMPORTANT CONSIDERATIONS FOR BILAYERS
50 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 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 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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83 Options to specify input files:
84 -f [<.xtc/.trr/…>] (traj.xtc)
86 Trajectory: xtc trr cpt gro g96 pdb tng
87 -n [<.ndx>] (index.ndx) (Optional)
89 Index file
90 -s [<.tpr>] (topol.tpr)
92 Portable xdr run input file
93 -ei [<.dat>] (electrons.dat) (Optional)
95 Generic data file
96 Options to specify output files:
98 -o [<.xvg>] (density.xvg)
100 xvgr/xmgr file
101 Other options:
103 -b <time> (0)
105 Time of first frame to read from trajectory (default unit ps)
106 -e <time> (0)
108 Time of last frame to read from trajectory (default unit ps)
109 -dt <time> (0)
111 Only use frame when t MOD dt = first time (default unit ps)
112 -[no]w (no)
114 View output .xvg, .xpm, .eps and .pdb files
115 -xvg <enum> (xmgrace)
117 xvg plot formatting: xmgrace, xmgr, none
118 -d <string> (Z)
120 Take the normal on the membrane in direction X, Y or Z.
121 -sl <int> (50)
123 Divide the box in this number of slices.
124 -dens <enum> (mass)
126 Density: mass, number, charge, electron
127 -ng <int> (1)
129 Number of groups of which to compute densities.
130 -[no]center (no)
132 Perform the binning relative to the center of the (changing)
133 box. Useful for bilayers.
134 -[no]symm (no)
136 Symmetrize the density along the axis, with respect to the cen‐
137 ter. Useful for bilayers.
138 -[no]relative (no)
140 Use relative coordinates for changing boxes and scale output by
141 average dimensions.
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144 · When calculating electron densities, atomnames are used instead of
145 types. This is bad.
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148 gmx(1)
149 More information about GROMACS is available at <‐
151 http://www.gromacs.org/>.
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154 2019, GROMACS development team
1552018.7 May 29, 2019 GMX-DENSITY(1)