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Journal Article

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

MPS-Authors
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Gapsys,  V.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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de Groot,  B. L.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Fulltext (public)

3071484.pdf
(Publisher version), 2MB

Supplementary Material (public)

3071484_Suppl.pdf
(Supplementary material), 3MB

Citation

Gapsys, V., & de Groot, B. L. (2019). Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife, 8: e44718. doi:10.7554/eLife.44718.


Cite as: http://hdl.handle.net/21.11116/0000-0003-D645-E
Abstract
A 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.