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

Gapsys, V.; de Groot, B. L.

doi:10.1101/563064

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bioRxiv · 10.1101/563064

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

Gapsys, V.·de Groot, B. L.

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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. Here, we express three main concerns about that study. In addition, we show 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.

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Gapsys, V., de Groot, B. L.. 2019-02-28. Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. https://doi.org/10.1101/563064

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