1 .TH g_density 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_density - calculates the density of the system
9 .BI "\-n" " index.ndx "
10 .BI "\-s" " topol.tpr "
11 .BI "\-ei" " electrons.dat "
12 .BI "\-o" " density.xvg "
14 .BI "\-[no]version" ""
28 \&Compute partial densities across the box, using an index file. Densities
29 \&in kg/m3, number densities or electron densities can be
30 \&calculated. For electron densities, a file describing the number of
31 \&electrons for each type of atom should be provided using \fB \-ei\fR.
32 \&It should look like:
36 \& atomname = nrelectrons
38 \& atomname = nrelectrons
40 \&The first line contains the number of lines to read from the file.
41 \&There should be one line for each unique atom name in your system.
42 \&The number of electrons for each atom is modified by its atomic
47 Trajectory: xtc trr trj gro g96 pdb cpt
49 .BI "\-n" " index.ndx"
53 .BI "\-s" " topol.tpr"
55 Run input file: tpr tpb tpa
57 .BI "\-ei" " electrons.dat"
61 .BI "\-o" " density.xvg"
67 Print help info and quit
69 .BI "\-[no]version" "no "
70 Print version info and quit
72 .BI "\-nice" " int" " 19"
75 .BI "\-b" " time" " 0 "
76 First frame (ps) to read from trajectory
78 .BI "\-e" " time" " 0 "
79 Last frame (ps) to read from trajectory
81 .BI "\-dt" " time" " 0 "
82 Only use frame when t MOD dt = first time (ps)
85 View output xvg, xpm, eps and pdb files
87 .BI "\-xvg" " enum" " xmgrace"
88 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
90 .BI "\-d" " string" " Z"
91 Take the normal on the membrane in direction X, Y or Z.
93 .BI "\-sl" " int" " 50"
94 Divide the box in nr slices.
96 .BI "\-dens" " enum" " mass"
97 Density: \fB mass\fR, \fB number\fR, \fB charge\fR or \fB electron\fR
99 .BI "\-ng" " int" " 1"
100 Number of groups to compute densities of
102 .BI "\-[no]symm" "no "
103 Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
105 .BI "\-[no]center" "no "
106 Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0.
109 \- When calculating electron densities, atomnames are used instead of types. This is bad.
114 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.