scholarly journals Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

2012 ◽  
Vol 116 (29) ◽  
pp. 8584-8603 ◽  
Author(s):  
Victor Ovchinnikov ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transitions ◽  
Targeted Molecular Dynamics ◽  
Dynamics Simulations

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
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

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.

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

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

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.

scholarly journals Estimation of Protein–Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

2019 ◽  
Vol 59 (12) ◽  
pp. 5135-5147 ◽  
Author(s):  
Steffen Wolf ◽  
Marta Amaral ◽  
Maryse Lowinski ◽  
Francois Vallée ◽  
Djordje Musil ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Targeted Molecular Dynamics ◽  
Dynamics Simulations ◽  
Non Equilibrium
Sign in / Sign up

Export Citation Format

Share Document