The good, the bad and the user in soft matter simulations
arXiv:1602.00466 · doi:10.1016/j.bbamem.2016.02.004
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.
References in corpus (5)
- Canonical sampling through velocity-rescaling
- Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
- Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
- Simple quantitative tests to validate sampling from thermodynamic ensembles
- Equilibration and Thermalization of Classical Systems
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