ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models

Arnold, Axel; Lenz, Olaf; Kesselheim, Stefan; Weeber, Rudolf; Fahrenberger, Florian; Roehm, Dominic; Košovan, Peter; Holm, Christian

doi:10.1007/978-3-642-32979-1_1

Cited by 181 publications

(146 citation statements)

References 41 publications

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“…The simulations were performed in the canonical ensemble using the ESPResSo package 53,54 . A total number of 1000 particles (500 dimers) where used.…”

Section: The Model and The Simulation Detailsmentioning

confidence: 99%

Self-Assembly and Water-like Anomalies in Janus Nanoparticles

2015

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We explore the pressure versus temperature phase diagram of dimeric Janus nanoparticles using Molecular Dynamics simulations. The nanoparticle was modeled as a dumbbells particle, and have one monomer that interacts by a standard Lennard Jones potential and another monomer that is modeled using a two-length scale shoulder potential. Monomeric and dimeric systems modeled by this shoulder potential show waterlike anomalies, and we investigate if a Janus nanoparticle composed by one anomalous monomer will exhibit anomalous behavior and self-assembly structures.The influence of the non-anomalous monomer in the dimeric system properties was explored. We show that the diffusion anomaly is maintained, while the density anomaly can disappear depending on the non-anomalous monomer characteristics . As well, the self-assembled structures are affected.Our results are discussed in the basis of the distinct monomer-monomer interactions and on the two-length scale fluid characteristics.

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“…The simulations were performed in the canonical ensemble using the ESPResSo package 53,54 . A total number of 1000 particles (500 dimers) where used.…”

Section: The Model and The Simulation Detailsmentioning

confidence: 99%

Self-Assembly and Water-like Anomalies in Janus Nanoparticles

2015

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“…Desmond (www.deshawresearch.com/resources_desmond.html) (Bowers et al, 2006) is a high-performance molecular dynamics simulation package. ESPResSo (extensible simulation package for research on soft matter; http://espressomd.org/) (Arnold et al, 2013;Limbach et al, 2006) is a simulation package specially focused on coarse-grained-particle simulations. GROMACS (Groningen machine for chemical simulation; www.gromacs.…”

Section: Box 2 Molecular Dynamics Force Fields and Software Packagesmentioning

confidence: 99%

Computational ‘microscopy’ of cellular membranes

Ingólfsson

Arnarez²,

Periole³

et al. 2016

Journal of Cell Science

136

120

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Computational 'microscopy' refers to the use of computational resources to simulate the dynamics of a molecular system. Tuned to cell membranes, this computational 'microscopy' technique is able to capture the interplay between lipids and proteins at a spatiotemporal resolution that is unmatched by other methods. Recent advances allow us to zoom out from individual atoms and molecules to supramolecular complexes and subcellular compartments that contain tens of millions of particles, and to capture the complexity of the crowded environment of real cell membranes. This Commentary gives an overview of the main concepts of computational 'microscopy' and describes the state-of-the-art methods used to model cell membrane processes. We illustrate the power of computational modelling approaches by providing a few in-depth examples of largescale simulations that move up from molecular descriptions into the subcellular arena. We end with an outlook towards modelling a complete cell in silico.

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“…We will limit ourselves here, however, to presenting only results for the case of N = 50 monomers per polymer arm, because the behavior for both shorter arms is qualitatively the same. Simulations were performed on single star-polymers using the ESPResSo package [31] with a Langevin thermostat and fixed center of mass. Since our goal is to describe the static properties of these systems, we choose the masses of all types of monomers to be the same.…”

Section: The Single-star Conformation Diagrammentioning

confidence: 99%

Self-assembly of magnetically functionalized star-polymer nano-colloids

Blaak

Likos

2018

Eur. Phys. J. E

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Abstract.We explore the potential of star-polymers that carry super-paramagnetic nano-particles as endgroups with respect to the single-molecule self-assembly process. With the aid of molecular dynamics simulation, the configurations of these macromolecules are analyzed as a function of functionality, magnetic interaction strength, and the length of the polymeric arms. By means of an external magnetic field the nano-particles can be controlled to form static or dynamic dipolar chains, resulting in conformations of isolated stars that can be characterized by the average number of chains and length. The single-molecule conformation diagram in the plane of magnetic interaction strength vs. the star-functionality is obtained. Further, the molecules are characterized by means of various shape and size order parameters.

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ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models

Cited by 181 publications

References 41 publications

Self-Assembly and Water-like Anomalies in Janus Nanoparticles

Self-Assembly and Water-like Anomalies in Janus Nanoparticles

Computational ‘microscopy’ of cellular membranes

Self-assembly of magnetically functionalized star-polymer nano-colloids

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