To determine the value of r in the flat bottom potential, it is usually set to the distance between the ion and the edge of the box, in the direction perpendicular to the flat bottom potential. In your case, if you want to confine the ions within one layer along the y-axis, then r would be half the box length along the y-axis.

To plot the potential resulting from the flat bottom potential, you can use the gmx potential command in GROMACS. This command calculates the interaction energy between a molecule and the simulation box as a function of position, and can be used to visualize the potential due to the flat bottom potential.

Flat bottom potential is a good option for confining ions within a specific region of the simulation box. Another approach that can be used is to use position restraints, which can be applied to specific atoms or groups of atoms to confine them to a specific region of space. However, this approach may be less effective for confining ions, as they can be mobile and may not stay within the restrained region.

Satyendra Singh I really appreciate your answer It helped me plot the potential.

But what I am getting is actually a regular position restrain potential instead of a flat-bottomed one - please check the figure below -. Is Gromacs taking the left edge of the box as R reference and that's what causing this behavior?

I am using the following syntax :

#ifdef POSRES

[ position_restraints ]

1 2 4 9.5 10000

#endif

Yes, it looks like Gromacs is applying a regular position restraint potential rather than a flat-bottomed one. The behavior you are seeing in the plot is consistent with a regular position restraint, where the potential increases linearly with distance from the reference point.

In order to apply a flat-bottomed restraint in Gromacs, you need to use the flat-bottom option in the position restraint file. The syntax for this option is:

codeflat-bottom-x flat-bottom-y flat-bottom-z

where flat-bottom-x, flat-bottom-y, and flat-bottom-z are the flat-bottom distances in the x, y, and z directions, respectively.

So, for example, if you want to apply a flat-bottomed restraint in the y direction with a flat-bottom distance of 9.5 nm, your position restraint file should look something like this:

code#ifdef POSRES [ position_restraints ] ; atom fx fy fz 1 0 10000 0 flat-bottom-9.5 0 0 2 0 10000 0 flat-bottom-9.5 0 0 4 0 10000 0 flat-bottom-9.5 0 0 #endif

Note that you also need to include the flat-bottom-9.5 option for the y component of the restraint.

As for the reference point for the restraint, Gromacs uses the origin (0, 0, 0) of the simulation box as the reference point by default. However, you can specify a different reference point by including an r_0 option in your position restraint file. For example:

code#ifdef POSRES [ position_restraints ] ; atom fx fy fz 1 0 10000 0 flat-bottom-9.5 0 0 r_0 0 5 0 2 0 10000 0 flat-bottom-9.5 0 0 r_0 0 5 0 4 0 10000 0 flat-bottom-9.5 0 0 r_0 0 5 0 #endif

This would set the reference point for the restraint to (0, 5, 0) instead of (0, 0, 0).

I am gonna try this new syntax and see the result, I really appreciate your help. But may you please refer me to where you got this syntax? because the manual does not really contain this information, neither the official topology file format.