[gmx-users] trans-membrane protein simulation
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
> Will it please be recommended to follow the* Justin tutorial *for membrane
> protein simulation (
> 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field combination in that tutorial is also really outdated and better force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.
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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