[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin A. Lemkul]

On 7/13/12 6:44 AM, J Peterson wrote:
> Thanks Justin,
>
> The explanations are very very useful during my course of simulating a
> protein with POPC.
>
> I also would like to get explanation on how to simulate a protein which has
> only its N-terminal region embedded in the membrane but the rest in solvent.
>
> What is the easy and accurate way to do it?
>

Position the protein with editconf -center and follow all the other steps in the 
same way.  The dimensions of the box become quite important in such a case. 
There are some general tips on such placement in another of my tutorials:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html

-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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