[gmx-users] Temperature in simulation

[Shima Arasteh]

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.





 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, October 3, 2012 5:18 PM
Subject: Re: [gmx-users] Temperature in simulation



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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