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Can martini used for simulation of protein's dissociation
- exianshine
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12 years 6 months ago #803
by exianshine
Can martini used for simulation of protein's dissociation was created by exianshine
I want to simulate a process of a multi units protein's deactiviation, which is the dissociation of the subunits of the protein.
Is it proper to use the elastic network for my protein's topology ?
Or should I leave the EN out ? Thanks a lot.
Is it proper to use the elastic network for my protein's topology ?
Or should I leave the EN out ? Thanks a lot.
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- djurre
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12 years 6 months ago #804
by djurre
Replied by djurre on topic Can martini used for simulation of protein's dissociation
Dear KONG Xian,
It is hard to say in general. You could try a short (~200ns) simulation of the protein without EN. If the protein falls apart (the rmsd goes up a lot), you will need an elastic network. But since you want to look at the dissociation of a sub-unit, make sure the elastic bands are not in-between the different sub-units!
If the rmsd stays low you could simulate without EN.
It is hard to say in general. You could try a short (~200ns) simulation of the protein without EN. If the protein falls apart (the rmsd goes up a lot), you will need an elastic network. But since you want to look at the dissociation of a sub-unit, make sure the elastic bands are not in-between the different sub-units!
If the rmsd stays low you could simulate without EN.
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