Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides

2017 ◽  
Vol 13 (10) ◽  
pp. 5039-5053 ◽  
Author(s):  
Philipp S. Schmalhorst ◽  
Felix Deluweit ◽  
Roger Scherrers ◽  
Carl-Philipp Heisenberg ◽  
Mateusz Sikora
Keyword(s):  
Force Field ◽  
Martini Force Field

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

2021 ◽  
Author(s):  
Christos Lamprakis ◽  
Ioannis Andreadelis ◽  
John Manchester ◽  
Camilo Velez-Vega ◽  
José S. Duca ◽  
...  
Keyword(s):  
Force Field ◽  
Protein Dimerization ◽  
Martini Force Field

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

scholarly journals ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

2020 ◽  
Vol 153 (4) ◽  
pp. 045103 ◽  
Author(s):  
Xiaohua Zhang ◽  
Shiv Sundram ◽  
Tomas Oppelstrup ◽  
Sara I. L. Kokkila-Schumacher ◽  
Timothy S. Carpenter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Accelerated Molecular Dynamics ◽  
Martini Force Field

scholarly journals Martini Coarse-Grained Models of Imidazolium-Based Ionic Liquids: From Nanostructural Organization to Liquid-Liquid Extraction

2020 ◽  
Author(s):  
Luis Itza Vazquez-Salazar ◽  
Michele Selle ◽  
Alex H. de Vries ◽  
Siewert-Jan Marrink ◽  
Paulo C. T. Souza
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Rational Design ◽  
Value Added ◽  
Liquid Extraction ◽  
Coarse Grained ◽  
Great Success ◽  
Liquid Liquid Extraction ◽  
Martini Force Field ◽  
Wide Range

<div> <div> <div> <p>Ionic liquids (IL) are remarkable green solvents, which find applications in many areas of nano- and biotechnology including extraction and purification of value-added compounds or fine chemicals. These liquid salts possess versatile solvation properties that can be tuned by modifications in the cation or anion structure. So far, in contrast to the great success of theoretical and computational methodologies applied to other fields, only a few IL models have been able to bring insights towards the rational design of such solvents. In this work, we develop coarse-grained (CG) models for imidazolium-based ILs using a new version of the Martini force field. The model is able to reproduce the main structural properties of pure ILs, including spatial heterogeneity and global densities over a wide range of temperatures. More importantly, given the high intermolecular compatibility of the Martini force field, this new IL CG model opens the possibility of large-scale simulations of liquid-liquid extraction experiments. As examples, we show two applications, namely the extraction of aromatic molecules from a petroleum oil model and the extraction of omega-3 polyunsaturated fatty acids from a fish oil model. In semi-quantitative agreement with the experiments, we show how the extraction capacity and selectivity of the IL could be affected by the cation chain length or addition of co-solvents. </p> </div> </div> </div>

scholarly journals Coarse-grained Simulation of Anionic Surfactant Sodium Dodecyl Sulfate

2021 ◽  
Author(s):  
Xiang-feng Jia ◽  
Jing-fei Chen ◽  
Hui-xue Ren ◽  
Qi Wang ◽  
Wen Xu ◽  
...  
Keyword(s):  
Force Field ◽  
Sodium Dodecyl ◽  
Coarse Grained ◽  
Inversion Method ◽  
Ionic Surfactant ◽  
Coarse Grained Model ◽  
Piecewise Function ◽  
Martini Force Field ◽  
Improved Model ◽  
Vdw Interaction

Abstract Through analyzing the deficiency of the current coarse-grained (CG) model, a new CG model for the ionic surfactant was proposed based on the Martini force field and iterative Boltzmann inversion method. In this model, the electrostatic interaction can be tackled by using a self-defined piecewise function to avoid the disadvantage of using coarse-grained solvents, and the VDW interaction parameters were derived by iterative methods. Using the improved model, the radial distribution function of NaCl and SDS solution in all-atom OPLS can be completely reproduced. The successful setup of the new coarse-grained model provides a good example of the construction of a high-precision coarse-grained force field.

Martini Force Field for Protonated Polyethyleneimine

2019 ◽  
Vol 41 (4) ◽  
pp. 349-361 ◽  
Author(s):  
Titus Adrian Beu ◽  
Andrada‐Elena Ailenei ◽  
Răzvan‐Ioan Costinaş
Keyword(s):  
Force Field ◽  
Martini Force Field

scholarly journals Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field

2020 ◽  
Vol 16 (4) ◽  
pp. 2550-2560 ◽  
Author(s):  
Hanif M. Khan ◽  
Paulo C. T. Souza ◽  
Sebastian Thallmair ◽  
Jonathan Barnoud ◽  
Alex H. de Vries ◽  
...  
Keyword(s):  
Force Field ◽  
Π Interactions ◽  
Martini Force Field

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

2015 ◽  
Vol 11 (9) ◽  
pp. 4486-4494 ◽  
Author(s):  
Yifei Qi ◽  
Helgi I. Ingólfsson ◽  
Xi Cheng ◽  
Jumin Lee ◽  
Siewert J. Marrink ◽  
...  
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Martini Force Field ◽  
Coarse Grained Simulations
Sign in / Sign up

Export Citation Format

Share Document