Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

eLife

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[1] Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany;

关键词: molecular dynamics;    thermodynamics;    kinetics;    box size;    hemoglobin;    Human;   

DOI  :  10.7554/eLife.44718

来源: publisher

【 摘 要 】

10.7554/eLife.44718.001A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

【 授权许可】

CC BY