1 .TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_potential - calculates the electrostatic potential across the box
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-n" " index.ndx "
10 .BI "\-s" " topol.tpr "
11 .BI "\-o" " potential.xvg "
12 .BI "\-oc" " charge.xvg "
13 .BI "\-of" " field.xvg "
15 .BI "\-[no]version" ""
27 .BI "\-[no]spherical" ""
29 .BI "\-[no]correct" ""
31 \&\fB g_potential\fR computes the electrostatical potential across the box. The potential is
32 \&calculated by first summing the charges per slice and then integrating
33 \&twice of this charge distribution. Periodic boundaries are not taken
34 \&into account. Reference of potential is taken to be the left side of
35 \&the box. It is also possible to calculate the potential in spherical
36 \&coordinates as function of r by calculating a charge distribution in
37 \&spherical slices and twice integrating them. epsilon_r is taken as 1,
38 \&but 2 is more appropriate in many cases.
42 Trajectory: xtc trr trj gro g96 pdb cpt
44 .BI "\-n" " index.ndx"
48 .BI "\-s" " topol.tpr"
50 Run input file: tpr tpb tpa
52 .BI "\-o" " potential.xvg"
56 .BI "\-oc" " charge.xvg"
60 .BI "\-of" " field.xvg"
66 Print help info and quit
68 .BI "\-[no]version" "no "
69 Print version info and quit
71 .BI "\-nice" " int" " 19"
74 .BI "\-b" " time" " 0 "
75 First frame (ps) to read from trajectory
77 .BI "\-e" " time" " 0 "
78 Last frame (ps) to read from trajectory
80 .BI "\-dt" " time" " 0 "
81 Only use frame when t MOD dt = first time (ps)
84 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
86 .BI "\-xvg" " enum" " xmgrace"
87 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
89 .BI "\-d" " string" " Z"
90 Take the normal on the membrane in direction X, Y or Z.
92 .BI "\-sl" " int" " 10"
93 Calculate potential as function of boxlength, dividing the box in nr slices.
95 .BI "\-cb" " int" " 0"
96 Discard first nr slices of box for integration
98 .BI "\-ce" " int" " 0"
99 Discard last nr slices of box for integration
101 .BI "\-tz" " real" " 0 "
102 Translate all coordinates distance in the direction of the box
104 .BI "\-[no]spherical" "no "
105 Calculate spherical thingie
107 .BI "\-ng" " int" " 1"
108 Number of groups to consider
110 .BI "\-[no]correct" "no "
111 Assume net zero charge of groups to improve accuracy
114 \- Discarding slices for integration should not be necessary.
119 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.