[gmx-users] Protein unfolded after COM pulling

[Yun Shi]

A general question:

In COM pulling (pull two molecules away), does the weakest
inter-molecular interaction always break first? Or is it the
interaction aligned on the pulling direction break first?

In other words, does every part of the molecule "feel" the pulling
force? Or the part close to the COM "feel" stronger force that the
part of molecule that is far away from its COM?

Thanks,
Yun

On Mon, Feb 4, 2013 at 6:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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).
>>
>
> Attachments to the list are prohibited; if you have files or images to share
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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
>
> --
> ========================================
>
> 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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