1g_potential(1)            GROMACS suite, VERSION 4.5            g_potential(1)
2
3
4

NAME

6       g_potential - calculates the electrostatic potential across the box
7
8       VERSION 4.5
9

SYNOPSIS

11       g_potential  -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc
12       charge.xvg -of field.xvg -[no]h -[no]version -nice int -b time -e  time
13       -dt  time  -[no]w  -xvg enum -d string -sl int -cb int -ce int -tz real
14       -[no]spherical -ng int -[no]correct
15

DESCRIPTION

17       Compute the electrostatical potential across the box. The potential  is
18       calculated  by first summing the charges per slice and then integrating
19       twice of this charge distribution. Periodic boundaries  are  not  taken
20       into  account.  Reference  of potential is taken to be the left side of
21       the box. It's also possible to calculate  the  potential  in  spherical
22       coordinates  as  function  of r by calculating a charge distribution in
23       spherical slices and twice integrating them. epsilon_r is taken as 1, 2
24       is more appropriate in many cases.
25

FILES

27       -f traj.xtc Input
28        Trajectory: xtc trr trj gro g96 pdb cpt
29
30       -n index.ndx Input
31        Index file
32
33       -s topol.tpr Input
34        Run input file: tpr tpb tpa
35
36       -o potential.xvg Output
37        xvgr/xmgr file
38
39       -oc charge.xvg Output
40        xvgr/xmgr file
41
42       -of field.xvg Output
43        xvgr/xmgr file
44
45

OTHER OPTIONS

47       -[no]hno
48        Print help info and quit
49
50       -[no]versionno
51        Print version info and quit
52
53       -nice int 19
54        Set the nicelevel
55
56       -b time 0
57        First frame (ps) to read from trajectory
58
59       -e time 0
60        Last frame (ps) to read from trajectory
61
62       -dt time 0
63        Only use frame when t MOD dt = first time (ps)
64
65       -[no]wno
66        View output xvg, xpm, eps and pdb files
67
68       -xvg enum xmgrace
69        xvg plot formatting:  xmgrace,  xmgr or  none
70
71       -d string Z
72        Take the normal on the membrane in direction X, Y or Z.
73
74       -sl int 10
75        Calculate  potential  as function of boxlength, dividing the box in nr
76       slices.
77
78       -cb int 0
79        Discard first nr slices of box for integration
80
81       -ce int 0
82        Discard last nr slices of box for integration
83
84       -tz real 0
85        Translate all coordinates distance in the direction of the box
86
87       -[no]sphericalno
88        Calculate spherical thingie
89
90       -ng int 1
91        Number of groups to consider
92
93       -[no]correctno
94        Assume net zero charge of groups to improve accuracy
95
96

KNOWN PROBLEMS

98       - Discarding slices for integration should not be necessary.
99
100

SEE ALSO

102       gromacs(7)
103
104       More  information  about  GROMACS  is  available  at   <http://www.gro‐
105       macs.org/>.
106
107
108
109                                Thu 26 Aug 2010                 g_potential(1)
Impressum