normal Test system for Martini v.3 ?

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2 years 11 months ago #8919 by glykos
Test system for Martini v.3 ? was created by glykos
We are trying to implement martini v.3 for simple protein+water+ions systems. Following the description in the SI file of the v.3 paper, we can run a simulation using the martinate + martinize combination. In the test system we are using (1ROP.pdb, a homodimeric 4-helix-bundle) the simulation performed with v.3 appears to be significantly less stable (structurally) compared to martini v.2.2. I am worried that we have messed-up the setup, and I'm looking for some results/benchmarks/case studies for a protein+water system in order to validate (or otherwise) what we are seeing locally.

Thanks a lot for any pointers/advice,
Nicholas

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2 years 10 months ago #8945 by riccardo
Replied by riccardo on topic Test system for Martini v.3 ?
Hi Nicholas, sorry for the slow reply.
did you try the small-molecule binding tutorial?
cgmartini.nl/index.php/martini-3-tutoria...all-molecule-binding
That explains how to set up a system similar to what you need.
It's no updated yet to latest Martini 3 version (it uses the open beta release) but with the info in the SI of the paper you should be able to set that up with the published Martini 3 version.

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2 years 10 months ago #8946 by glykos
Replied by glykos on topic Test system for Martini v.3 ?
Thanks a lot, I'll try that !

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