Individual Ion Activity Coefficients in Aqueous Electrolytes from Explicit-Water Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Sina Hassanjani Saravi ◽  
Athanassios Z. Panagiotopoulos
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Activity Coefficients ◽  
Aqueous Electrolytes ◽  
Individual Ion ◽  
Ion Activity ◽  
Dynamics Simulations ◽  
Explicit Water

scholarly journals Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

2012 ◽  
Vol 8 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Jens Kleinjung ◽  
Walter R. P. Scott ◽  
Jane R. Allison ◽  
Wilfred F. van Gunsteren ◽  
Franca Fraternali
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Implicit Solvation ◽  
Solvation Parameters ◽  
Dynamics Simulations ◽  
Explicit Water

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

2007 ◽  
Vol 26 (2) ◽  
pp. 571-580 ◽  
Author(s):  
Phanourios Tamamis ◽  
Spiros S. Skourtis ◽  
Dimitrios Morikis ◽  
John D. Lambris ◽  
Georgios Archontis
Keyword(s):  
Molecular Dynamics ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Explicit Water

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

2007 ◽  
Vol 44 (1-3) ◽  
pp. 150
Author(s):  
Georgios Archontis ◽  
Phanourios Tamamis ◽  
Spiros S. Skourtis ◽  
Dimitrios Morikis ◽  
John D. Lambris
Keyword(s):  
Molecular Dynamics ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Explicit Water

scholarly journals Combining enhanced sampling with experiment-directed simulation of the GYG peptide

2018 ◽  
Vol 17 (03) ◽  
pp. 1840007 ◽  
Author(s):  
Dilnoza B. Amirkulova ◽  
Andrew D. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Parallel Tempering ◽  
Collective Variables ◽  
Novel Approach ◽  
Sampling Problem ◽  
Combination Of Methods ◽  
Dynamics Simulations ◽  
Explicit Water

Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.

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