1g_density(1)              GROMACS suite, VERSION 4.5              g_density(1)
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NAME

6       g_density - calculates the density of the system
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8       VERSION 4.5
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SYNOPSIS

11       g_density  -f  traj.xtc  -n index.ndx -s topol.tpr -ei electrons.dat -o
12       density.xvg -[no]h -[no]version -nice int -b  time  -e  time  -dt  time
13       -[no]w  -xvg  enum  -d  string  -sl  int  -dens  enum -ng int -[no]symm
14       -[no]center
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DESCRIPTION

17       Compute partial densities across the box, using an index  file.  Densi‐
18       ties  in  kg/m3,  number  densities or electron densities can be calcu‐
19       lated. For electron densities, a file describing the  number  of  elec‐
20       trons  for  each type of atom should be provided using  -ei.  It should
21       look like:
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23          2
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25          atomname = nrelectrons
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27          atomname = nrelectrons
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29       The first line contains the number of lines  to  read  from  the  file.
30       There should be one line for each unique atom name in your system.  The
31       number of electrons for each atom is modified  by  its  atomic  partial
32       charge.
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FILES

35       -f traj.xtc Input
36        Trajectory: xtc trr trj gro g96 pdb cpt
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38       -n index.ndx Input, Opt.
39        Index file
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41       -s topol.tpr Input
42        Run input file: tpr tpb tpa
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44       -ei electrons.dat Input, Opt.
45        Generic data file
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47       -o density.xvg Output
48        xvgr/xmgr file
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OTHER OPTIONS

52       -[no]hno
53        Print help info and quit
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55       -[no]versionno
56        Print version info and quit
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58       -nice int 19
59        Set the nicelevel
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61       -b time 0
62        First frame (ps) to read from trajectory
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64       -e time 0
65        Last frame (ps) to read from trajectory
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67       -dt time 0
68        Only use frame when t MOD dt = first time (ps)
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70       -[no]wno
71        View output xvg, xpm, eps and pdb files
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73       -xvg enum xmgrace
74        xvg plot formatting:  xmgrace,  xmgr or  none
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76       -d string Z
77        Take the normal on the membrane in direction X, Y or Z.
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79       -sl int 50
80        Divide the box in nr slices.
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82       -dens enum mass
83        Density:  mass,  number,  charge or  electron
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85       -ng int 1
86        Number of groups to compute densities of
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88       -[no]symmno
89        Symmetrize  the  density  along  the axis, with respect to the center.
90       Useful for bilayers.
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92       -[no]centerno
93        Shift the center of mass along the axis to zero. This  means  if  your
94       axis  is  Z  and  your box is bX, bY, bZ, the center of mass will be at
95       bX/2, bY/2, 0.
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KNOWN PROBLEMS

99       - When calculating electron densities, atomnames are  used  instead  of
100       types. This is bad.
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SEE ALSO

104       gromacs(7)
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106       More   information  about  GROMACS  is  available  at  <http://www.gro‐
107       macs.org/>.
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111                                Thu 26 Aug 2010                   g_density(1)
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