normal Holliday Junction Conformational Changes?

  • jonasori
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2 years 8 months ago #5733 by jonasori
Hello again everybody,

Does Martini allow for conformational changes in a Holliday junction? My intuition would be that it does not, and a couple long-ish runs that I've done have agreed with that, but I thought it would be best to learn it from the people who actually know.

Thanks, as always.

~Jonas

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2 years 8 months ago #5734 by jaakko
Replied by jaakko on topic Holliday Junction Conformational Changes?
Hi Jonas,

There won't be any major conformational changes with the stiff elastic network. Soft network won't work out of the box with Holliday junctions so one would need to device a EN specifically for Holliday junctions if more conformation freedom is needed.

- Jaakko

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2 years 7 months ago #5767 by jonasori
Replied by jonasori on topic Holliday Junction Conformational Changes?
Hi Jaakko,

Sorry I never responded to this. That's great to know - thanks.

Jonas

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