Does anyone know if there are some good courses where you can learn modeling and/or molecular dynamics simulations for the non-experienced user??
Most of the commercial vendors offer training courses, or you might be able to take a class or two at a local university (e.g. http://fusion.mssm.edu/gradschool/descript.cfm?cname=19&snum=1 )
Sybyl (now Accelrys): http://www.accelrys.com/training/
ACS sometimes offers classes as well.