The Hitchhiker’s guide to molecular dynamics

This lecture aims at advanced (master’s, PhD) students in physics, chemistry, physical chemistry, biochemistry, engineering (and possibly biology) who use, or plan to use, molecular dynamics (MD) computer simulations in the course of their research work. This lecture is, however, neither (or only in a very limited way) a course on the scientific background of this method (quantum mechanics, statistical mechanics, computational methods), nor is it a pragmatics tutorial (‘how-to’ guide) which button to click on some graphical interface or other. We rather aim at pointing out to the aspiring user of any kind of simulation software some of the important choices that must be made as well as some of the problems and pitfalls that he or she may encounter on the way to reliable and meaningful scientific results. This includes a few reminders what not to forget to avoid such mistakes and possibly where to look to correct them if they have, unavoidably, been made.