[gmx-users] Temperature in simulation

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Oct 3 20:02:41 CEST 2012

You are right and I will insert the native protein in membrane. To do so, I want to set the temperature of nvt.mdp file to 300 K, however I want to use the result output of memrane simulated in 310 K for 50 ns. 
Through your earlier suggestions, I got that velocities would be reassigned in new simulation and 10 degree is not a thing to be concerned in my system. 
Here, I'd like to know if I am criticized for using this difference between temperatures?
Thanks for all your suggestions, that are all kind of you :-)


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, October 3, 2012 8:44 PM
Subject: Re: [gmx-users] Temperature in simulation

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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