scholarly journals All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer

Langmuir ◽  
2011 ◽  
Vol 27 (17) ◽  
pp. 10523-10537 ◽  
Author(s):  
Jason D. Perlmutter ◽  
William J. Drasler ◽  
Wangshen Xie ◽  
Jiali Gao ◽  
Jean-Luc Popot ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Protein ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

scholarly journals CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5934
Author(s):  
Alessandro Marchetto ◽  
Zeineb Si Chaib ◽  
Carlo Alberto Rossi ◽  
Rui Ribeiro ◽  
Sergio Pantano ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Protein ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Biological Macromolecules ◽  
Martini Force Field ◽  
Dynamics Simulations ◽  
Automated Protocol ◽  
Computational Platform ◽  
Coarse Grained Molecular Dynamics

Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.

Adsorption-induced co-assembly of hairy and isotropic particles

2020 ◽  
Vol 22 (16) ◽  
pp. 8757-8767
Author(s):  
Tomasz Staszewski ◽  
Małgorzata Borówko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We use coarse-grained molecular dynamics simulations to study the behavior of polymer-tethered particles immersed in fluids of isotropic particles.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

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