On 10/3/12 9:39 AM, Shima Arasteh wrote:
Hi all,
I want to insert a protein in POPC lipid bilayer.
First of all, I simulated POPC in water in 310 K. Now, I want to insert protein
in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300
K and then go on. Does anybody know it would be incorrect logically ?
Well, what is the goal of your simulation? If you're trying to simulate a
physiological environment (human body/cells) then 310 K is the correct
temperature. If you're trying to replicate some other in vitro conditions, that
should motivate your choice.
As I know, 10 degree increase in temperature of system, may result in some
troubles in my small protein. But I guess this would not happen for lipid
bilayer.
A 10 K increase shouldn't affect the protein dynamics all that strongly. What
problems have you seen, and why do you expect them to carry over to a membrane
environment? One of the most important factors in choosing the temperature of a
lipid bilayer is the phase transition temperature of the lipids. POPC should be
fluid at either 300 K or 310 K, so that is not a concern.
-Justin
--
========================================
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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