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:
- Solution of the PBE with an inhomogeneous dielectric (1.0 inside the ion
and 78.54 outside)
- 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.