CHARMM

CHARMM is a versatile software package primarily designed for molecular dynamics simulations of proteins, nucleic acids and lipids. CHARMM incorporates a large number of specialized and advanced methods. It uses script language based input files.

Links

CHARMM official web site (documentation and forum):
http://www.charmm.org

CHARMM GUI:
http://www.charmm-gui.org

CHARMM Tutorials:
http://www.charmmtutorial.org/index.php/CHARMM_Tutorial
http://www.mdy.univie.ac.at/lehre/charmm/course1/course1-1.html

CHARMM workshop:
http://www.psc.edu/general/software/packages/charmm/tutorial/index.html

Other molecular dynamics tutorials:
http://www.ch.embnet.org/MD_tutorial