title: The good, the bad and the user in soft matter simulations.
abstract: 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. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
authors: Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand. Electronic address: jirasak.w@ku.ac.th.
authors: Jirasak
authors: J
authors: Wong-Ekkabut
authors: Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, MetaForum, 5600 MB Eindhoven, the Netherlands. Electronic address: mkarttu@tue.nl.
authors: Mikko
authors: M
authors: Karttunen
mesh_terms: D016477:Artifacts; D056004:Molecular Dynamics Simulation; D037742:Nanotubes, Carbon / Q000737:chemistry; D017510:Protein Folding; D055672:Static Electricity
chemical_list: D037742:Nanotubes, Carbon
keywords: Artifacts; Membranes; Molecular dynamics; Simulation protocols; Simulations