[gmx-users] Protein unfolded after COM pulling

Yun Shi yunshi09 at gmail.com
Tue Feb 5 03:32:01 CET 2013

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).

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.

Thanks for any suggestion.


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