[gmx-users] Protein unfolded after COM pulling

[Justin Lemkul]

On 2/4/13 9:32 PM, Yun Shi wrote:
> Hi all,
>
> I am pulling one monomer of a tetrameric protein away from the other
> three monomers with pull_k1 = 10000 and pull_rate1 = 0.0005.
>
> As shown in the attached picture, the green monomer (being pulled) has
> unfolded while two regions on it are still interacting with the other
> three monomers at the end of my pulling simulations (13 ns, so COM
> distance has been pulled 6.5 nm).
>

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> If I want to calculate deltaG of this process, can I use distance
> restraints on the green monomer being pulled to maintain its folded
> structure? Otherwise, I will have to construct a larger box or pull
> even slower than 0.5 nm/ns.
>

Yes, you probably need distance restraints.  Complex restraints often fail with 
domain decomposition, so you may need to use particle decomposition instead.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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