On 7/10/12 6:09 AM, Shima Arasteh wrote:
Dear gmx users,
I want to simulate a protein in bilayer. The chosen bilayer is POPC.
According to Justin's tutorial about KALP15 in DPPC, I would simulate the
protein in lipid bilayer and water. In this tutorial I didn't find the
simulation of bilayer in water seperately and it is just going through the
simulation with protein.
See part 1 of step 3:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
It's not a full simulation of a membrane, but it presents all the essential
elements - coordinate file, topology (very simple), and .mdp (though it is for
EM, not an MD simulation).
I need to say that I got the POPC.itp and .top through the link sent me by
dear Peter.
Now I'm wondering if POPC is needed to simulate in water before applying in
simulation of protein in POPC?
The answer depends on how well equilibrated the starting structure is. If
you're going to be putting a protein in it, you'll have to re-equilibrate that
new system for a considerable amount of time, so simulating the membrane
beforehand may or may not be relevant, but a thoroughly equilibrated membrane
will reduce the time needed in equilibrating the membrane protein system.
-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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