What can we Learn from Molecular Dynamics Simulations of Macromolecular Liquids?

1989 ◽  
Vol 177 ◽  
Author(s):  
Gary S. Grest ◽  
Kurt Kremer ◽  
Michael Murat
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamic Properties ◽  
Star Polymers ◽  
Coarse Grained ◽  
Linear Polymers ◽  
Coarse Grained Model ◽  
Percolation Clusters ◽  
Large Systems ◽  
Dynamics Simulations

ABSTRACTWe describe how molecular dynamics simulations for a relatively simple coarse grained model can be very useful for investigating the static and dynamic properties of polymers and other macromolecular liquids. We show that it is important to use a simplified coarse grained model instead of a detailed microscopic model if one is interested in studying on modern supercomputers large systems which also relax slowly. As examples we present results for isolated star polymers with f-arms and diluted gelation/percolation clusters. We find in agreement with recent neutron scattering experiments that diluted percolation clusters swell and that their fractal dimension is reduced from 2.5 to 2. We also discuss our results for a dense melt of entangled linear polymers to show that the method is effective at high density. Our results for the entangled melt cover the crossover from Rouse to reptation and strongly support the concept of reptation.

A coil-to-globule transition capable coarse-grained model for poly(N-isopropylacrylamide)

2020 ◽  
Vol 22 (32) ◽  
pp. 17913-17921
Author(s):  
H. A. Pérez-Ramírez ◽  
G. Odriozola
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Isopropyl Acrylamide ◽  
Dynamics Simulations

We present a model for mesoscopic molecular dynamics simulations of poly(N-isopropyl-acrylamide) (pNIPAM).

scholarly journals A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level

2020 ◽  
Vol 48 (5) ◽  
pp. e29-e29 ◽  
Author(s):  
Jürgen Walther ◽  
Pablo D Dans ◽  
Alexandra Balaceanu ◽  
Adam Hospital ◽  
Genís Bayarri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Web Interface ◽  
Harmonic Model ◽  
Coarse Grained Model ◽  
Mesoscopic Models ◽  
Dynamics Simulations ◽  
Helical Parameters ◽  
High Computational Efficiency

Abstract We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.

Coarse-grained molecular dynamics simulations of α-1,3-glucan

Soft Matter ◽  
2019 ◽  
Vol 15 (23) ◽  
pp. 4669-4681 ◽  
Author(s):  
Daniel J. Beltran-Villegas ◽  
Daniel Intriago ◽  
Kyle H. C. Kim ◽  
Natnael Behabtu ◽  
J. David Londono ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Monomer Structure ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

In this work we present a coarse-grained model for α-1,3-glucan that captures hydrogen bonding directionality and polysaccharide monomer structure.

scholarly journals Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

2016 ◽  
Vol 472 (2186) ◽  
pp. 20150556 ◽  
Author(s):  
Radek Erban
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Brownian Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Computational Domain ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

Sign in / Sign up

Export Citation Format

Share Document