[gmx-users] Protein unfolded after COM pulling
jalemkul at vt.edu
Tue Feb 5 03:35:19 CET 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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