normal Go-MARTINI dimer

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8 months 6 days ago - 8 months 6 days ago #9692 by shaukat_i
Go-MARTINI dimer was created by shaukat_i
Hi everyone,

If I want to simulate a protein dimerization (starting state is monomers) or protein dimer (stating state is dimer):
for the first case If I use Go potentials independently on monomers and then start simulating, I should see the conformational dynamics.

But for the second case, should I use the --merge flag to generate Go virtual bonds between the subunits? Does it work - has anyone used it?

As I could not find a relevant section in the protein-dimer tutorial, I am not sure how to proceed.
Tutorial page: cgmartini.nl/index.php/2021-martini-onli...ced#protein-membrane

Please let me know our thoughts, references if anyone has done these trials.
Thank you.
Last edit: 8 months 6 days ago by shaukat_i. Reason: added a link of tutorial I am currently referring to.

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7 months 3 weeks ago #9699 by adolfom
Replied by adolfom on topic Go-MARTINI dimer
I think the contact map generally account for the contact between two sub-units (or more). One can use this CM for the generation of virtual sites as well as the Go bond between chains. There are no more virtual sites. They are only defined for each site in the residue in each chain. So one can also edit the itp file to include some additional Go bond between chains.
best,

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