[gmx-users] trans-membrane protein simulation

Justin Lemkul jalemkul at vt.edu
Mon Aug 7 16:37:27 CEST 2017

On 8/6/17 10:25 PM, Amir Zeb wrote:
> Hello gmx-users!
> I want to simulate a membrane protein, where it sets across the membrane
> (means that some of the protein's region lays outside the membrane and is
> water exposed). Obviously, the protein will be experiencing two different
> environments like membrane and water (heterogeneous condition) during the
> simulation.
> Will it please be recommended to follow the* Justin tutorial *for membrane
> protein simulation (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
> or I should make some modifications to this tutorial? Also, please suggest

In your case, don't center the protein to coincide with the center of the 
membrane (you'll have to figure out how it needs to be positioned).  The force 
field combination in that tutorial is also really outdated and better force 
fields exist.  The tutorial remains as is because it is a useful illustration of 
possible methods to build such systems and how force field files are organized. 
That doesn't mean you should do exactly as it does for your real scientific work.

> me whether this kind of simulation in heterogeneous condition is worth
> enough to get reliable data or not?

People do simulations like this all the time.  They generally need to be very 
long (hundreds of ns) to capture both protein and lipid dynamics.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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