Dear Pooria,

As one example, Gromacs allows you to include the presence of an electric field. Here you have an example (of many you can find):

https://www.diva-portal.org/smash/get/diva2:410123/FULLTEXT01.pdf

http://thread.gmane.org/gmane.science.biology.gromacs.user/83069

For sure, other MD codes like LAMMPS and NAMD include it as well.

Regarding the shapes you mention, I would imagine in Gromacs you could insert for instance a sphere and give it its own potential.

Bests,

Andrés.

I suggest LAMMPS can be run in Windows as well.

if quantum level, quantum espresso, BO