[gmx-users] Protein unfolded after COM pulling

[Justin Lemkul]

On 2/7/13 12:40 PM, Yun Shi wrote:
> 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?
>

Probably both.  Whatever you do with SMD is path-dependent.

> 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?
>

Forces are interpolated onto other parts of the structure, but as stated above, 
whichever way you pull has implications for the outcome.  It's not an 
equilibrium process.

-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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