I want to study the interaction of protein with functionalized nanotube by QM/MM calculations. Would you please introduce me some user friendly and accurate packages for this purpose(exceot Gaussian) and beginners? It's better to be free(for students).
Gromacs ==> http://www.gromacs.org/Documentation/How-tos/QMMM
Amber ==> (http://ambermd.org)
Discovery Studio, Material Studio are commercial packages
As you want a free package, you could use GROMACS which was mentioned earlier. Similarly, LAMMPS is also a versatile free package.
Use the following article that can provide you some details.
Article QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO...
https://sites.google.com/site/piccininsimone/reserarch_projects/QMMM
AMBER is not a free package, however, you could use ambertools to generate files and then can convert in GROMACS format. I am not sure though about QM/MM. Someone might help you help you out with that.
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