Multiple Steering Molecular Dynamics Applied to Water Exchange at Alkali Ions

2002 ◽  
Vol 106 (50) ◽  
pp. 13027-13032 ◽  
Author(s):  
Michele Cascella ◽  
Leonardo Guidoni ◽  
Amos Maritan ◽  
Ursula Rothlisberger ◽  
Paolo Carloni
Keyword(s):  
Molecular Dynamics ◽  
Water Exchange ◽  
Alkali Ions

scholarly journals Enhancing Water Sampling of Buried Binding Sites Using Nonequilibrium Candidate Monte Carlo

2020 ◽  
Author(s):  
Teresa Danielle Bergazin ◽  
Ido Ben-Shalom ◽  
Nathan M. Lim ◽  
Samuel C. Gill ◽  
Michael K. Gilson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Binding Sites ◽  
Water Exchange ◽  
Free Energy Calculations ◽  
Water Molecules ◽  
Water Sampling ◽  
Computer Aided Drug Design ◽  
Practical Applications ◽  
Computer Aided

<div>Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our NCMC/MD method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.</div>

scholarly journals Hydration of alkali ions from first principles molecular dynamics revisited

2007 ◽  
Vol 126 (3) ◽  
pp. 034501 ◽  
Author(s):  
Takashi Ikeda ◽  
Mauro Boero ◽  
Kiyoyuki Terakura
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Alkali Ions ◽  
First Principles Molecular Dynamics

scholarly journals Enhancing Water Sampling of Buried Binding Sites Using Nonequilibrium Candidate Monte Carlo

2020 ◽  
Author(s):  
Teresa Danielle Bergazin ◽  
Ido Ben-Shalom ◽  
Nathan M. Lim ◽  
Samuel C. Gill ◽  
Michael K. Gilson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Binding Sites ◽  
Water Exchange ◽  
Free Energy Calculations ◽  
Water Molecules ◽  
Water Sampling ◽  
Computer Aided Drug Design ◽  
Practical Applications ◽  
Computer Aided

<div>Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our NCMC/MD method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.</div>

Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

2016 ◽  
Vol 18 (44) ◽  
pp. 30323-30333 ◽  
Author(s):  
Yi-Jung Tu ◽  
Matthew J. Allen ◽  
G. Andrés Cisneros
Keyword(s):  
Molecular Dynamics ◽  
Exchange Rates ◽  
Molecular Dynamics Simulations ◽  
Water Exchange ◽  
Experimental Results ◽  
Lanthanide Ions ◽  
Ethyl Sulfate ◽  
Dynamics Simulations

Molecular dynamics simulations have been carried out to explain the water-exchange rates of lanthanide ions in water and water/[EMIm][EtSO4] observed from 17O-NMR experiments. Our simulations are in agreement with experimental results with respect to water-exchange trends.

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