[gmx-users] simulation of a simple, solvated DPPC membrane

[Justin A. Lemkul]

undergrad j wrote:
> Hello there!
> 
> I am an undergraduate working on my thesis, which involves the 
> simulation of a DPPC membrane. My college is small and the department 
> does not have experience with MD simulations, so I am 100% on my own. I 
> have successfully modeled simple proteins in water- but I want to move 
> onto bilayers.
> 
> I am attempting to simulate a simple, homogeneous DPPC bilayer. I have a 
> .pdb file of the membrane, along with  .itp files provided by 
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I 
> am following this procedure for setting up the membrane:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html
> 
> However, I feel like I am missing something? The procedure is telling me 
> to alter a .top file to accommodate the altered force field .itp's 
> (ffG53a6 to include Berger lipid parameters-which I have already 
> accomplished)- maybe the .top in question is the topology of the protein 
> that is being implanted in the membrane? I do not want a membrane bound 
> protein in this simulation- so how do I generate a .top for a simple 
> membrane? Is it through pdb2gmx? Do I have to manually program the 
> system topology?
> 
> Maybe someone can point me to a detailed procedure for setting up a 
> simple membrane system from start to finish...?
> 

A suitable topology for a DPPC-only system is provided as part of my tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/topol_dppc.top

It's rather simple and does not require pdb2gmx, just the extended 53a6 force 
field.  If you've already got that, you're just about done.

-Justin

> I am probably going to be bugging this group a lot in the next few 
> weeks- thank you for reading this....
> 
> (Sorry if this question is confusing/sounds silly- again, I'm working on 
> my own)
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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