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Molecular Mechanics/Coarse-grained (MM/CG) is a hybrid model proposed in
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.
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:
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A recent release version of the TRUNK code that include also some complete examples can be downloaded here.