[gmx-users] POPC in water

[Justin A. Lemkul]

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

-- 
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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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