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Post by Ali on Aug 2, 2021 6:22:32 GMT
Hello,
What are the differences between Mcell3 and Mcell4? In simulation, I got Error due to different requirements of Mcell4 comparing Mcell3.
Thank you in advance.
Ali
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Post by Adam on Aug 2, 2021 15:03:38 GMT
Hello,
thank you for your questions.
There are a few main differences:
- the simulation space is limited with MCell4 and the simulation box is set in panel partitioning
- releases based on some event (such as a reaction or a wall hit occuring) must be now defined through callbacks in Python code
- periodic boundary conditions as they were in MCell3 are not supported
- MCell3 scripting in CellBlender won't work anymore
Otherwise your MCell3 model should work just fine.
Could you post here the exact message you got?
Thank you,
Adam
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Post by Ali Salam on Aug 3, 2021 13:14:57 GMT
Hello Adam,
thank you. The error: Molecule s escaped the simulation area defined by partition size. Diffused m...try object box that keeps all molecules within given area.... Another option is to increase partition size.
Bests regards,
Ali
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Post by Adam on Aug 3, 2021 15:55:08 GMT
Hello Ali,
ok, thank you for the error message.
In this case, ther error is related to this difference:
- the simulation space is limited with MCell4 and the simulation box is set in panel partitioning
What happened is that a molecule diffuse outside of the simulated volume.
The way how to fix this is to put a large box arouind your molecules to make sure that all stay within this box.
By default the box will be reflective, but you can set it as absorptive if you would like the molecules to disappear (https://mcell.org/tutorials/surf_class_surf_mol.html).
Hope this helps,
Adam
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