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

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.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-D645-E Version Permalink: http://hdl.handle.net/21.11116/0000-0003-D649-A
Genre: Journal Article

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 Creators:
Gapsys, V.1, Author              
de Groot, B. L.1, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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Free keywords: box size; hemoglobin; human; kinetics; molecular biophysics; molecular dynamics; structural biology; thermodynamics
 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.

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Language(s): eng - English
 Dates: 2019-06-20
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.7554/eLife.44718
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Title: eLife
Source Genre: Journal
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Pages: 10 Volume / Issue: 8 Sequence Number: e44718 Start / End Page: - Identifier: -