[gmx-users] Temperature in simulation

[Justin Lemkul]

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

-- 
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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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