APBS Tutorial
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Born solvation energies: effect of radius

This section presents the series of calculations that will be carried out to examine the effect of ion radius on electrostatic potential and solvation energy. Specifically, this generates a set of ions with different radii and uses APBS, together with the above input file, to solve Poisson's equation.

This example uses a Bash shell script to run a series of APBS calculations and generate a series of Gnuplot graphs. First, you will need to download the archive containing the Bash script and the template input files here.

Once the input files are downloaded, they need to be extracted from the archive:

        $ gzip -dc born.tar.gz | tar xvf -

This script can then be executed by typing:

        $ bash runme.sh

While running, the script will generate a series of plots generated from the APBS output depicting the change in electrostatic potential as a function of distance from the ion center. Of particular interest is the change in potential from the inside to the outside of the ion. When finished, the run will generate a summary plot of solvation energy as a function of distance. The total run time for this script was roughly 6 minutes on a 2.2 GHz Intel Pentium 4.

In addition to the graphical output, users should also examine the various files generated by the script, including:

apbs-##.in: APBS input files for each radius (##)
ion-##.pqr: Ion PQR files for each radius (##)
apbs-##.out: APBS output files for each radius (##)
potential-##.dx: Raw OpenDX-format potential data for each radius (##)
potential-##-xaxis.dx: Potential data along x-axis for each radius (##)
energy.dat: Solvation energies for each energy calculated

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