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

TL;DR

This review discusses common errors and artifacts in molecular dynamics simulations across various fields, emphasizing the importance of proper practices and validation to improve reliability and accuracy.

Contribution

It provides a practical overview of errors in MD simulations and offers guidance on avoiding artifacts, serving as a starting point for researchers to improve simulation reliability.

Findings

Identification of common sources of errors in MD simulations

Guidelines for avoiding artifacts and improving practices

Encouragement for validation and careful checking of simulation setups

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.