How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations

2014 ◽  
Vol 118 (13) ◽  
pp. 3572-3581 ◽  
Author(s):  
Hugo A. L. Filipe ◽  
Maria João Moreno ◽  
Tomasz Róg ◽  
Ilpo Vattulainen ◽  
Luís M. S. Loura
Keyword(s):  
Free Energy ◽  
Lipid Membranes ◽  
Energy Simulations ◽  
Membrane Deformations

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

scholarly journals Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations

2018 ◽  
pp. 53-90 ◽  
Author(s):  
Daniel Roston ◽  
Xiya Lu ◽  
Dong Fang ◽  
Darren Demapan ◽  
Qiang Cui
Keyword(s):  
Free Energy ◽  
Phosphoryl Transfer ◽  
Energy Simulations

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

1998 ◽  
Vol 275 (5) ◽  
pp. 823-846 ◽  
Author(s):  
Georgios Archontis ◽  
Thomas Simonson ◽  
Dino Moras ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Specific Amino Acid ◽  
Energy Simulations ◽  
Amino Acid Recognition
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