SIESTA is free for academic institutions, you only have to register and activate your account with an official address. I haven't worked with it in the last three years, but at that time it was running only on linux.

It is an ab initio molecular dynamics simulation package, with good manuals, which is valuable for starters. It also has tutorials and a user forum, where you can post your questions.

I don't have much hands-on experience with other simulation packages, however Siesta isn't a black box, where you can put some numbers in and get results out. You'll have to optimize your parameters like pseudopotentials and basis sets to start with. Overall it's well worth a look.

http://departments.icmab.es/leem/Siesta/

Dear Özlem,

Thank you very much for your interest.

I will examine SIESTA software but I do not use linux.

Best Regards

If you have the underlying equations with parameters available I suggest you can try to use a general purpose dynamical simulation software like Modelica. There are both commercial and free implementations of Modelica. I myself use JModelica from Lund  in Sweden. It works for Windows (and also for Linux and Mac). See http://www.jmodelica.org