[gmx-users] Temperature in simulation

[Justin Lemkul]

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

-- 
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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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