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Internals - Methods

MM/CG

    Molecular Mechanics/Coarse-grained (MM/CG) is a hybrid model proposed in

    M. Neri, et al. Phys. Rev. Lett. 95(21), 218102 (2005)

    to combine both accuracy of full-atom MD and low cost of CG simulations. In this approach, the binding site is described by an atomistic potential (the GROMOS96), whilst the rest of the protein is treated with a coarse-grain potential (the Go-like model). In the new version of the method, available on both the local clusters and based on Gromacs 4.5.1, two artificial potentials were introduced to avoid the water diffusing away or into the hydrophobic part of membrane. The first sends the molecules back to the system, while the second mimics the membrane action on the protein. Using this approach, the time needed to perform simulations reduces more than ten times in comparison to full-atom MD simulations.


Ion Channel CG model

    Coarse-Grain model of ion channels that predicts selectivity using particle-particle Coloumb interactions and the induced surface charges at the channel-protein/water boundary:

    Finnerty J. J., et al. 9(1), 766-773 (2013)

    Development work at the German Research School for Simulation Sciences is focused on extending the model to include structural information for the charged side chains.
    The most up to date code and documentation can be found on the German Research School for Simulation Sciences Redmine server at the page:

     

    https://jay.grs.rwth-aachen.de/redmine/projects/ionch

    To get access this server you need to be authorized by the German Research School for Simulation Sciences IT service: send an email to the German Research School for Simulation Sciences helpdesk to get the sufficient credentials.

    A recent release version of the TRUNK code that include also some complete examples can be downloaded here.