[gmx-users] Re: problem in g_membed

[Justin Lemkul]

On 7/29/13 9:10 AM, pavithrakb wrote:
> sir,
> the reason for selecting POPE doesn't have much valid reason. I mean, I have
> referred previous works and in the recent work they have used POPE membrane
> for my protein (the exact protein) simulation. I have searched literature on
> selecting a membrane for simulation to know/understand why they have
> selected the particular membrane. But couldn't find put the reason why?.

The choice of a membrane is nearly as significant as the choice of the force 
field that represents the system.  The chosen lipid model should be 
representative of the membrane environment that the protein will most likely 
experience.  POPE is common for bacterial membranes, while POPC is common for 
eukaryotic systems.  More complex models (rafts, etc) exist in the literature 
and are relevant in some cases.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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