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Building an MD Simulation Program
2013In this chapter, we will focus on how to build a molecular dynamics (MD) simulation program using three important parameters for an atom: forces, velocities and positions. There are many different equations available for calculating the parameters of an atom in an MD simulation program, depending on the level of the accuracy that we would like to ...
Melvin Choon Giap Lim, ZhaoWei Zhong
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Molecular dynamics (MD) simulations for polymers
Journal of Physics: Condensed Matter, 1990The authors review some recent MD simulations for polymer melts. For the melt chains of up to six entanglement lengths are taken into account. The data strongly support the reptation picture.
Kremer, K., Grest, G.
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MD Simulations and X-Ray Scattering
In the present chapter, the link between Molecular Dynamics, one of the most renowned simulation techniques in the world of statistical physics, and X-Ray diffraction, probably the most powerful and non-destructive technìque to assess the structure of materials of any kind, is examined. After a brief survey of classical (force field-based) and quantumGontrani L. +4 more
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MD Simulation of a Phospholipid Bilayer
2000We report first results of a molecular dynamics simulation of a fully hydrated dipalmitoyl-sn-glycero-phosphatidylcholin (DPPC) bilayer using the NγT-ensemble. Because of the large size of the simulated system, a parallel version of the simulation package MOSCITO [1] has been developed, which employs a dynamic loadbalancing algorithm to ensure uniform ...
Ralf Schmelter, Alfons Geiger
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MD Simulations of Nanomachining Monocrystalline Silicon
Key Engineering Materials, 2015Molecular dynamics (MD) simulations of nanomachining of monocrystalline silicon were performed with the aid of Tersoff potential. The effects of machining conditions on the nature of heat distribution and corresponding phase transformation during nanomachining were investigated.
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Electroporation of archaeal lipid membranes using MD simulations
Bioelectrochemistry, 2014Molecular dynamics (MD) simulations were used to investigate the electroporation of archaeal lipid bilayers when subjected to high transmembrane voltages induced by a charge imbalance, mimicking therefore millisecond electric pulse experiments. The structural characteristics of the bilayer, a 9:91 mol% 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo ...
Andraž, Polak +7 more
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ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles
Langmuir, 2019Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and ...
Mohammadreza Samieegohar +3 more
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Web-based MD Simulations using MoSGrid
2014CELLmicrocosmos neXt Workshop in context of the "German Conference on Bioinformatics" : Proceedings, CELLmicrocosmos neXt Workshop in context of the "German Conference on Bioinformatics", Bielefeld, 28.09 ...
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Quantum simulation of 2D antiferromagnets with hundreds of Rydberg atoms
Nature, 2021Pascal Scholl +2 more
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Tools for quantum simulation with ultracold atoms in optical lattices
Nature Reviews Physics, 2020Florian Schäfer +2 more
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