scholarly journals Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems

2016 ◽  
Vol 12 (3) ◽  
pp. 1360-1367 ◽  
Author(s):  
Albert C. Pan ◽  
Thomas M. Weinreich ◽  
Stefano Piana ◽  
David E. Shaw
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Complex Protein ◽  
Order Of Magnitude ◽  
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 On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Berk Hess ◽  
David van der Spoel ◽  
Mark J. Abraham ◽  
Erik Lindahl
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Error Cancellation ◽  
Wide Range ◽  
Order Of Magnitude ◽  
Dynamics Simulations

<div><div><div><p>Molecular dynamics is expected to produce accurate results over a wide range of conditions and timescales. However, this is not always the case since the field has been too reluctant to abandon historically popular techniques known to introduce artefacts. Two recent papers have suggested there are reliability issues in the GROMACS code since it no longer uses a legacy twin-range algorithm. Here, we show there are order-of-magnitude differences in accuracy favoring the modern Trotter decomposition, and that a force field relying on the old algorithm will have errors parametrized into the force field. Similarly, the suggestions about incorrect virial calculations turn out to be explained by insufficient accuracy in the default SHAKE settings used for GROMOS, while the GROMACS default choices are accurate. This highlights the importance of being more critical to error cancellation in simulations in order for algorithms and parameters to both gradually converge to more perfect ones.</p></div></div></div>

Reactivity of aldehydes at the air–water interface. Insights from molecular dynamics simulations and ab initio calculations

2015 ◽  
Vol 13 (6) ◽  
pp. 1673-1679 ◽  
Author(s):  
Marilia T. C. Martins-Costa ◽  
Francisco F. García-Prieto ◽  
Manuel F. Ruiz-López
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Computer Simulations ◽  
Rate Constant ◽  
Water Interface ◽  
Air Water Interface ◽  
Order Of Magnitude ◽  
Dynamics Simulations

Computer simulations show that solvation effects at the air–water interface significantly influence the chemistry of aldehydes, enhancing for instance the benzaldehyde photolysis rate constant by one order of magnitude.

scholarly journals On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Berk Hess ◽  
David van der Spoel ◽  
Mark J. Abraham ◽  
Erik Lindahl
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Error Cancellation ◽  
Wide Range ◽  
Order Of Magnitude ◽  
Dynamics Simulations

<div><div><div><p>Molecular dynamics is expected to produce accurate results over a wide range of conditions and timescales. However, this is not always the case since the field has been too reluctant to abandon historically popular techniques known to introduce artefacts. Two recent papers have suggested there are reliability issues in the GROMACS code since it no longer uses a legacy twin-range algorithm. Here, we show there are order-of-magnitude differences in accuracy favoring the modern Trotter decomposition, and that a force field relying on the old algorithm will have errors parametrized into the force field. Similarly, the suggestions about incorrect virial calculations turn out to be explained by insufficient accuracy in the default SHAKE settings used for GROMOS, while the GROMACS default choices are accurate. This highlights the importance of being more critical to error cancellation in simulations in order for algorithms and parameters to both gradually converge to more perfect ones.</p></div></div></div>

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