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Post by Eilen on Jun 21, 2021 18:51:12 GMT
Hello,
I ran the simulation and got a warning (see below). What does it mean? Error: x partitions closer than interaction diameter x partition #2 at -1 x partition#3 at interaction diameter 10.
Thank you.
Eilen
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Post by Adam on Jun 22, 2021 1:13:54 GMT
Hi Eilen, this is related to two settings: 1) the interaction radius (under panel Run Simulation -> Advanced Options -> Interaction Radius) and 2) partitioning step (under panel Partitions -> checked Include Partitions -> X/Y/Z Step) First thing that seems pretty high to me is the interaction radius being 10 um. The default interaction radius is computed from surface grid dentity like this: 1/sqrt(PI * surface_grid_density). The surface_grid_density says how many receptors fit on 1 um^2 of a membrane. If yor values of either the interaction radius itself or of surface_grid_density are set correctly, I would suggest to increase the paritioning X/Y/Z steps to values higher than the SQRT(2) * interaction radius. Little more information can be found in section 4.5: mcell.org/documentation/MCellQuickReferenceGuide.pdfIf this won't help, please let us know. Adam
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