normal elnedyn modifications

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3 months 1 week ago #7798 by bakerj
bakerj created the topic: elnedyn modifications
Hi all,

We are working on some simulations of a protein where there is a region of helix that is speculated to readily elongate under force compared to other regions (it is already partially disordered). Would it be reasonable to modify the Elnedyn elastic network and either weaken or remove some of the elastic bonds on the CG particles in that partially disordered region in order to capture some aspects of that conformational change? Will tweaking the Elnedyn elastic bonds cause other problems that I might not be anticipating?

Thanks,
Joe

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3 months 1 week ago #7804 by bart
bart replied the topic: elnedyn modifications
Though this is all dependent on the amount of distortion you expect, the transition of secondary structures is poorly or not captured at all in martini 2. Maybe you could have some better luck using martini with a go model. But for unraveling of a protein, you are in the grey area of using martini.

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