Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study

2007 ◽  
Vol 127 (17) ◽  
pp. 175105 ◽  
Author(s):  
César Augusto F. de Oliveira ◽  
Donald Hamelberg ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Accelerated Molecular Dynamics ◽  
Explicit Solvent ◽  
Kinetic Rates ◽  
Dynamics Simulations ◽  
Alanine Dipeptide

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

2020 ◽  
Vol 22 (15) ◽  
pp. 8021-8034
Author(s):  
Daniel Sadowsky ◽  
J. Samuel Arey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Ionic Solutes

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water.

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