scholarly journals Comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’

2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot

AbstractA 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.

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot

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.


2017 ◽  
Vol 4 (10) ◽  
pp. 1679-1690 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Esmat Mehrjouei ◽  
Amir Nasser Shamkhali ◽  
Mohsen Abbaspour ◽  
Sirous Salemi ◽  
...  

Molecular dynamics simulations were used to investigate the structural evolution and thermal behavior of Ni–Pd hollow nanoparticles.


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