Try Gromacs. It's good for classical and QM/MM simulations. It also has ready made functions that analyse the trajectory for thermodynamic and transport properties. To get it right, I suggest the tutorial page in gromacs webpage http://www.gromacs.org/Documentation/Tutorials. All the best and Happy computing !!!

Hello,

Try Gromacs it is free and easy to use, you have to just follow the guideline provided in the manual of gromacs. One more thing gromacs works best on linux platform you may use Ubuntu for the same.

For biomolecular systems, I know AMBER, NAMD, and GROMACS have been commonly used.

Thank you all for the recommendations.

MDynaMix also.