Ion-ion potential of mean force (PMF)

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In this example, we will look at the electrostatic potential, solvation energies, and solvation forces associated with two Born ions. In this case, we are interested in the effect of desolvation on the energetics of the system. The electrostatic potential is determined directly from solutions to the Poisson-Boltzmann equation (PBE). The solvation energies/forces are obtained from two calculations:

  1. Solution of the PBE with an inhomogeneous dielectric (1.0 inside the ion and 78.54 outside)
  2. Solution of the PBE with a homogeneous dielectric (1.0 everywhere)
The solvation energy/force is defined as the difference of the energies from these two calculations.

To run this example, type:

bash runme.sh

In this directory, you will find:

apbs.in
APBS input script for the PBE calculations; "RADIUS" should be replaced with the desired Born atom radius.
complex.pqr
PQR (structure) file of ion complex automatically generated by runme.sh
index.html
This file.
mol1.pqr
PQR (structure) file of stationary ion automatically generated by runme.sh
mol2.pqr
PQR (structure) file of mobile ion automatically generated by runme.sh
runme.sh
BASH script to run this example.
template.gnuplot
Template Gnuplot input file.