The file 'sample.dat' corresponds to a cytochrome c3 molecule, which
contains both protonatable and redox sites (4 heme groups). It was obtained
from Poisson-Boltzmann calculations using meadTools
(www.itqb.unl.pt/simulation).

The 'sample.out' file was produced using the following command:

petit-gcc -H 0,14,1 -T 300 -c 2.0 -q 1000 100000 < sample.dat > sample.out

Note that the executable was compiled with the '-O3' switch. Changing the
optimization level can produce slightly different results on certain
systems.

The output file contains different types of information (see README file),
which can be easily extracted using simple command-line parsing. See the
meadTools tutorial for an example involving only protonatable sites.

Since there are redox sites in cytochrome c3, you can also vary the
electrostatic potential of the solution through the option -E (e.g., "-E
-400,0,50"). In that case, potential dependencies are also included in the
output file, from which we can extract titration surfaces, E-dependent
pKhalfs, pH-dependent Ehalfs, etc (see refs in README).

