Do free computer programs exist that can simulate drug permeability in bacterial membranes?
I currently work alongside many biologists that are working on simulations of anti-microbial peptides in the membrane. These seem to have a similar mechanism to what you're aiming for &mdash; permeating the lipid bilayer. 

Presumably you have already come to the conclusion that molecular dynamic simulations are probably a good shot for exploring what may happen at an atomistic and energetic level. Software does exist, but an accurate answer from a project like this may take months of work and time on an HPC cluster. 

The only software recommended by PDB (trustworthy) explicitly for membrane systems is GROMACS (and it's free!). This has documentation on membrane simulation which I have used in the past. However you will need to be very careful in both designing the simulation and analyzing the output, and an expert guiding hand may be required.