Dear Martini 3 users:
I would like to define beads for the attached structure but I have no idea how to define appropriate atoms and bead types, especially for the C in the middle with 4 carbons attached to it. Could you please help me with that?
Thanks for your consideration.
Hi Mohammad,
I don't think it's possible to determine the bead types easily.
First look at the martini DB (https://mad.ibcp.fr/force_fields).
If you cannot find it there, you need to know if there is any experimental or All-atom simulation data regarding this molecule. There are some approaches, but at the end, you have to show your model works (through a series of tests including free energy validation)
1- I suggest you go through this paper first:
"Martini 3 Coarse-Grained Force Field: Small Molecules"
2- If you can break it apart and find Martini itp files for some building blocks of it, I suggest you start there. (consulting this link: https://github.com/ricalessandri/Martini3-small-molecules/blob/main/tutorials/building_block_table.pdf)
This is called "Parametrizing a new molecule based on known fragments" You can find more info here, in the first section:
http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/parametrzining-new-molecule-gmx5
3- If you have the all-atom simulation data, you can check the second section of the link above.
4- There are some other tools such as VOTCA (https://www.votca.org/csg/input_files.html) But I have not used them.
Please tell us how it went.
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