1GMX-POTENTIAL(1)                    GROMACS                   GMX-POTENTIAL(1)
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NAME

6       gmx-potential - Calculate the electrostatic potential across the box
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SYNOPSIS

9          gmx potential [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
10                       [-o [<.xvg>]] [-oc [<.xvg>]] [-of [<.xvg>]] [-b <time>]
11                       [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
12                       [-d <string>] [-sl <int>] [-cb <int>] [-ce <int>]
13                       [-tz <real>] [-[no]spherical] [-ng <int>] [-[no]correct]
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DESCRIPTION

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

26       Options to specify input files:
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28       -f [<.xtc/.trr/…>] (traj.xtc)
29              Trajectory: xtc trr cpt gro g96 pdb tng
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31       -n [<.ndx>] (index.ndx)
32              Index file
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34       -s [<.tpr>] (topol.tpr)
35              Portable xdr run input file
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37       Options to specify output files:
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39       -o [<.xvg>] (potential.xvg)
40              xvgr/xmgr file
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42       -oc [<.xvg>] (charge.xvg)
43              xvgr/xmgr file
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45       -of [<.xvg>] (field.xvg)
46              xvgr/xmgr file
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48       Other options:
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50       -b <time> (0)
51              Time of first frame to read from trajectory (default unit ps)
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53       -e <time> (0)
54              Time of last frame to read from trajectory (default unit ps)
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56       -dt <time> (0)
57              Only use frame when t MOD dt = first time (default unit ps)
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59       -[no]w (no)
60              View output .xvg, .xpm, .eps and .pdb files
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62       -xvg <enum> (xmgrace)
63              xvg plot formatting: xmgrace, xmgr, none
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65       -d <string> (Z)
66              Take the normal on the membrane in direction X, Y or Z.
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68       -sl <int> (10)
69              Calculate potential as function of boxlength, dividing  the  box
70              in this number of slices.
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72       -cb <int> (0)
73              Discard this number of  first slices of box for integration
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75       -ce <int> (0)
76              Discard this number of last slices of box for integration
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78       -tz <real> (0)
79              Translate  all  coordinates by this distance in the direction of
80              the box
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82       -[no]spherical (no)
83              Calculate in spherical coordinates
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85       -ng <int> (1)
86              Number of groups to consider
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88       -[no]correct (no)
89              Assume net zero charge of groups to improve accuracy
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KNOWN ISSUES

92       · Discarding slices for integration should not be necessary.
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SEE ALSO

95       gmx(1)
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97       More    information    about    GROMACS    is    available    at     <‐
98       http://www.gromacs.org/>.
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101       2019, GROMACS development team
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1062019.2                           Apr 16, 2019                 GMX-POTENTIAL(1)
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