In an MD simulation of a hydrophobic brush layer on a pure metal surface one can investigate in direct comparison where water and other substances are distributed under the chosen conditions. The study of longer sequences allows to derive the thermodynamic equilibrium (mean preferred location) as well as the dynamics (diffusion: how fast are sites exchanged).
Hydrophobic coatings can be applied by hydrophobic substances, e.g. so called brush layers. Mostly they are bound chemically after they have been brought to the surface, such that wear of the molecular brushes is low. Those who never have seen such a simulation model by their own eyes, would be surprised by the quick motions, that quick that only little measuring methods could capture them at all.
A simple measure for the quality of the brush layer is the contact angle of an applied water droplet. The more it comes close to 180 degrees, the more hydrophobic the surface is.
For historical reasons these two software-packages are related, although there development has become quite different nowadays. The GRO they have common in name in both cases goes back to the origin of the University of Groningen in the Netherlands.
GROMOS was an initiative of Prof. Herman J. C. Berendsen and Wilfred van Gunsteren and was already in the version of GROMOS85 an attempt and with GROMOS87 a succes for the simulation of biological molecules. After the move of Prof. van Gunsteren to ETH Zurich the package GROMOS96 and even its current successor was developped in Zurich. GROMOS is available commercially and for a symbolic fee also to the academic world. It has been challenged by its professional application in basic sciencific research, but requests for a large amount of detailed knowledge by its users. We at xirrus know about the advantages of the models of GROMOS96 and apply them as we require. Additionally we develop our own parameter sets. Gromacs has been initiated in the more quiet phases of GROMOS-application and has been branched off as individual package completely. The focus has been set to Open Source and always speed optimisation and method implementation was in the foreground. Gromacs has like any other package its own flaws. Numerous tricks are necessary to let a complex system run as we’d like to design it. But Gromacs runs on nearly all CPU architectures without much complications when the set-up could be established.
simulates your complex problem based on particles
Since 2001 we transfer our natural scientific knowledge to complex problems in software development. Since 2004 we offer simulations as a service for all those, who do not own the capacity or don’t have access to in-house resources for Molecular Dynamics and other particle problems (communication networks, traffic flow, congestion phenomenon) or many more other individuals or actor systems simulations.
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