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]center]
14                       [-[no]symm] [-[no]correct]
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DESCRIPTION

17       gmx  potential  computes  the electrostatical potential across the box.
18       The potential is calculated by first summing the charges per slice  and
19       then integrating twice of this charge distribution. Periodic boundaries
20       are not taken into account. Reference of potential is taken to  be  the
21       left side of the box. It is also possible to calculate the potential in
22       spherical coordinates as function of r by calculating a charge  distri‐
23       bution  in  spherical  slices  and twice integrating them. epsilon_r is
24       taken as 1, but 2 is more appropriate in many cases.
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26       Option -center performs the histogram binning and potential calculation
27       relative  to  the center of an arbitrary group, in absolute box coordi‐
28       nates. If you are calculating profiles along the Z axis  box  dimension
29       bZ,  output  would be from -bZ/2 to bZ/2 if you center based on the en‐
30       tire system.  Option -symm symmetrizes the output  around  the  center.
31       This will automatically turn on -center too.
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OPTIONS

34       Options to specify input files:
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36       -f [<.xtc/.trr/...>] (traj.xtc)
37              Trajectory: xtc trr cpt gro g96 pdb tng
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39       -n [<.ndx>] (index.ndx)
40              Index file
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42       -s [<.tpr>] (topol.tpr)
43              Portable xdr run input file
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45       Options to specify output files:
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47       -o [<.xvg>] (potential.xvg)
48              xvgr/xmgr file
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50       -oc [<.xvg>] (charge.xvg)
51              xvgr/xmgr file
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53       -of [<.xvg>] (field.xvg)
54              xvgr/xmgr file
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56       Other options:
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58       -b <time> (0)
59              Time of first frame to read from trajectory (default unit ps)
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61       -e <time> (0)
62              Time of last frame to read from trajectory (default unit ps)
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64       -dt <time> (0)
65              Only use frame when t MOD dt = first time (default unit ps)
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67       -[no]w (no)
68              View output .xvg, .xpm, .eps and .pdb files
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70       -xvg <enum> (xmgrace)
71              xvg plot formatting: xmgrace, xmgr, none
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73       -d <string> (Z)
74              Take the normal on the membrane in direction X, Y or Z.
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76       -sl <int> (10)
77              Calculate  potential  as function of boxlength, dividing the box
78              in this number of slices.
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80       -cb <int> (0)
81              Discard this number of  first slices of box for integration
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83       -ce <int> (0)
84              Discard this number of last slices of box for integration
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86       -tz <real> (0)
87              Translate all coordinates by this distance in the  direction  of
88              the box
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90       -[no]spherical (no)
91              Calculate in spherical coordinates
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93       -ng <int> (1)
94              Number of groups to consider
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96       -[no]center (no)
97              Perform  the  binning  relative  to the center of the (changing)
98              box. Useful for bilayers.
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100       -[no]symm (no)
101              Symmetrize the density along the axis, with respect to the  cen‐
102              ter. Useful for bilayers.
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104       -[no]correct (no)
105              Assume net zero charge of groups to improve accuracy
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KNOWN ISSUES

108       • Discarding slices for integration should not be necessary.
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SEE ALSO

111       gmx(1)
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113       More     information    about    GROMACS    is    available    at    <‐
114       http://www.gromacs.org/>.
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117       2022, GROMACS development team
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1222022.2                           Jun 16, 2022                 GMX-POTENTIAL(1)
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