The good, the bad and the user in soft matter simulations

J. Wong-ekkabut, M. Karttunen

Research output: Contribution to journalArticleAcademicpeer-review

64 Citations (Scopus)

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.".

Original languageEnglish
Pages (from-to)2529–2538
Number of pages10
JournalBiochimica et Biophysica Acta, Biomembranes
Volume1858
Issue number10
DOIs
Publication statusPublished - 7 Feb 2016

Keywords

  • Artifacts
  • Membranes
  • Molecular dynamics
  • Simulation protocols
  • Simulations

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