scholarly journals Improvement of Sampling Efficiency through Combined use of Molecular Dynamics Simulations with Implicit and Explicit Solvent Models

2013 ◽  
Vol 104 (2) ◽  
pp. 170a-171a ◽  
Author(s):  
Hiroko X. Kondo ◽  
Noriaki Okimoto ◽  
Makoto Taiji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Efficiency ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Combined Use ◽  
Dynamics Simulations ◽  
Implicit And Explicit

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.

scholarly journals Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides

2020 ◽  
Vol 16 (4) ◽  
pp. 2561-2569 ◽  
Author(s):  
Plamen Dobrev ◽  
Sahithya Phani Babu Vemulapalli ◽  
Nilamoni Nath ◽  
Christian Griesinger ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics
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