normal Modeling of the shear flow on the membrane

  • James Starlight
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2 months 6 hours ago #7328 by James Starlight
James Starlight created the topic: Modeling of the shear flow on the membrane
Dear MARTINI Users!

I am using a molecular dynamics simulation for the investigation of influence of shear flow on the oligomerisation of membrane proteins . My question: is it possible to model shear flow (e.g using some pressure coupling methods), as a directed force acting on the upper leaflet of CG membrane in X-Y directions, thus producing directed acceleration of water along the membrane?

Thanks for help!

James

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1 month 3 weeks ago #7335 by James Starlight
James Starlight replied the topic: Modeling of the shear flow on the membrane
UPDATE: any algorithms for the simulation of the membrane deformation in martini models (e.g using gromacs pooling code) will be appreciated here !!

James

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1 month 3 weeks ago #7343 by peterkroon
peterkroon replied the topic: Modeling of the shear flow on the membrane
This is not really a Martini question (try the Gromacs userlist), and I don't know of anyone in the lab doing anything like this.
Keep in mind that however you are going to implement this, the removal of linear CoM motion is going to be a problem to some degree.

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