[gmx-users] Protein unfolded after COM pulling

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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