[gmx-users] Protein unfolded after COM pulling

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 18:45:34 CET 2013

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


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