Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field

2018 ◽  
Vol 122 (4) ◽  
pp. 1516-1524 ◽  
Author(s):  
Pallavi Banerjee ◽  
Sudip Roy ◽  
Nitish Nair
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Infinite Dilution ◽  
Coarse Grained ◽  
Martini Force Field ◽  
Coarse Grained Molecular Dynamics

scholarly journals Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

2010 ◽  
Vol 114 (13) ◽  
pp. 4471-4485 ◽  
Author(s):  
Gia G. Maisuradze ◽  
Patrick Senet ◽  
Cezary Czaplewski ◽  
Adam Liwo ◽  
Harold A. Scheraga
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Force Field ◽  
Coarse Grained ◽  
Coarse Grained Molecular Dynamics

scholarly journals Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations

Polymers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 4044
Author(s):  
Jiramate Kitjanon ◽  
Wasinee Khuntawee ◽  
Saree Phongphanphanee ◽  
Thana Sutthibutpong ◽  
Nattaporn Chattham ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Quantitative Agreement ◽  
Filler Loading ◽  
Coarse Grained ◽  
Experimental Result ◽  
High Wear Resistance ◽  
Mechanical And Thermal Properties ◽  
Interfacial Interactions ◽  
Martini Force Field

The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0–32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.

scholarly journals Estimating Factors Determining Emulsification Capability of Surfactant-Like Peptide with Coarse-Grained Molecular Dynamics Simulation

2019 ◽  
Vol 19 (3) ◽  
pp. 599 ◽  
Author(s):  
Tegar Wijaya ◽  
Rukman Hertadi
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Martini Force Field ◽  
Underlying Principle ◽  
Hydropathy Index ◽  
Hydrophobic Tail ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The ability of surfactant-like peptides to emulsify oil has become the main focus of our current study. We predicted the ability of a series of surfactant-like peptides (G6D, A6D, M6D, F6D, L6D, V6D, and I6D) to emulsify decane molecules using coarse-grained molecular dynamics simulations. A 1-μs simulation of each peptide was carried out at 298 K and 1 atm using MARTINI force field. Simulation system was constructed to consist of 100 peptide molecules, 20 decane molecules, water, antifreeze particles and neutralizing ions in a random configuration. Out of seven tested peptides, M6D, F6D, L6D, V6D, and I6D were able to form emulsion while G6D and A6D self-assembled to order b-strands. A higher hydropathy index of amino acids constituting the hydrophobic tail renders the formation of an emulsion by peptides more likely. By calculating contact number between peptides and decanes, we found that emulsion stability and geometry depends on the structure of amino acids constituting the hydrophobic tail. Analysis of simulation trajectory revealed that emulsions are formed by small nucleation following by fusion to form a bigger emulsion. This study reveals the underlying principle at the molecular level of surfactant peptide ability to form an emulsion with hydrophobic molecules.

scholarly journals Coarse-grained molecular dynamics study of the self-assembly of polyphilic bolaamphiphiles using the SAFT-γ Mie force field

2021 ◽  
Author(s):  
Maziar Fayaz-Torshizi ◽  
Erich A. Müller
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Molecular Models ◽  
Coarse Grained Molecular Dynamics

A methodology is outlined to parametrize coarse grained molecular models for the molecular dynamics simulation of liquid crystals.

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.

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