Direct folding simulation of α-helices and β-hairpins based on a single all-atom force field with an implicit solvation model

2006 ◽  
Vol 66 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Soonmin Jang ◽  
Eunae Kim ◽  
Youngshang Pak
Keyword(s):  
Force Field ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Folding Simulation ◽  
Implicit Solvation Model

scholarly journals Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model

2018 ◽  
Vol 39 (22) ◽  
pp. 1707-1719 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Fang-Yu Lin ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model ◽  
Poisson Boltzmann

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

2006 ◽  
Vol 2 (2) ◽  
pp. 420-433 ◽  
Author(s):  
Asim Okur ◽  
Lauren Wickstrom ◽  
Melinda Layten ◽  
Raphäel Geney ◽  
Kun Song ◽  
...  
Keyword(s):  
Replica Exchange ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model

scholarly journals KECSA-Movable Type Implicit Solvation Model (KMTISM)

2015 ◽  
Vol 11 (2) ◽  
pp. 667-682 ◽  
Author(s):  
Zheng Zheng ◽  
Ting Wang ◽  
Pengfei Li ◽  
Kenneth M. Merz
Keyword(s):  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model

scholarly journals Assessment of Constant-Potential Implicit Solvation Calculations of Electrochemical Energy Barriers for H2 evolution on Pt

2018 ◽  
Author(s):  
Maxime Van den Bossche ◽  
Egill Skúlason ◽  
Christoph Rose-Petruck ◽  
Hannes Jonsson
Keyword(s):  
Electrostatic Interactions ◽  
Computational Cost ◽  
Electrochemical Reactions ◽  
Critical Importance ◽  
Theoretical Estimation ◽  
H2 Evolution ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model ◽  
Constant Potential

Theoretical estimation of the activation energy of electrochemical reactions is of critical importance but remains challenging. In this work, we address the usage of an implicit solvation model for describing hydrogen evolution reaction steps on Pt(111) and Pt(110), and compare with the `extrapolation' approach as well as single-crystal measurements. We find that both methods yield qualitatively similar results, which are in fair agreement with the experimental data. Care should be taken, however, in addressing spurious electrostatic interactions between periodically repeated slabs in the VASPsol implementation. Considering the lower computational cost and higher flexibility of the implicit solvation approach, we expect this method to become a valuable tool in electrocatalysis.<br>

Assessment of Constant-Potential Implicit Solvation Calculations of Electrochemical Energy Barriers for H2 evolution on Pt

2018 ◽  
Author(s):  
Maxime Van den Bossche ◽  
Egill Skúlason ◽  
Christoph Rose-Petruck ◽  
Hannes Jonsson
Keyword(s):  
Electrostatic Interactions ◽  
Computational Cost ◽  
Electrochemical Reactions ◽  
Critical Importance ◽  
Theoretical Estimation ◽  
H2 Evolution ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model ◽  
Constant Potential

Theoretical estimation of the activation energy of electrochemical reactions is of critical importance but remains challenging. In this work, we address the usage of an implicit solvation model for describing hydrogen evolution reaction steps on Pt(111) and Pt(110), and compare with the `extrapolation' approach as well as single-crystal measurements. We find that both methods yield qualitatively similar results, which are in fair agreement with the experimental data. Care should be taken, however, in addressing spurious electrostatic interactions between periodically repeated slabs in the VASPsol implementation. Considering the lower computational cost and higher flexibility of the implicit solvation approach, we expect this method to become a valuable tool in electrocatalysis.<br>

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