  Molecular dynamics (MD) simulations have become popular in materials science,
biochemistry, biophysics and several other fields. Improvements in
computational resources, in quality of force field parameters and algorithms
have yielded significant improvements in performance and reliability. On the
other hand, no method of research is error free. In this review, we discuss a
few examples of errors and artifacts due to various sources and discuss how to
avoid them. Besides bringing attention to artifacts and proper practices in
simulations, we also aim to provide the reader with a starting point to explore
these issues further. In particular, we hope that the discussion encourages
researchers to check software, parameters, protocols and, most importantly,
their own practices in order to minimize the possibility of errors. The focus
here is on practical issues.
