A coarse-grained model of dimethyl sulfoxide for molecular dynamics simulations with lipid membranes

2020 ◽  
Vol 153 (3) ◽  
pp. 035104
Author(s):  
Shobhna ◽  
Monika Kumari ◽  
Hemant K. Kashyap
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Lipid Membranes ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamics Simulations

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.

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