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 <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
