[gmx-users] Temperature in simulation
jalemkul at vt.edu
Wed Oct 3 19:14:05 CEST 2012
On 10/3/12 10:16 AM, Shima Arasteh wrote:
> Actually, I want to study this system of protein-membrane, trying to replicate in vitro conditions and then studying function of the protein.
> I simulated the protein in water to see the usual result : losing its native configuration. Then, I am trying to insert the protein in membrane to study its function.
Inserting an unfolded (or partially unfolded) protein into a membrane and hoping
it reflects reality may or may not be wise. If you want to compare water vs.
membrane environments, those should be two separate simulations, both starting
from the same (presumably) native state of the protein. If you're hoping that
the protein will re-fold within the membrane, you're probably making a large
number of assumptions, most of which may not hold up under scrutiny.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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