[gmx-users] lipid tail order

[Justin Lemkul]

On 10/17/13 4:57 AM, Archana Sonawani-Jagtap wrote:
> Hi,
>
> I want to plot
> 1.  -SCD (lipid tail order parameters) profile for both the chains (sn1 and
> sn2)
>
> 2. Lateral diffusion of lipids
>
> 3. density profiles
>
>   in presence and absence of peptide.
>
> I have plotted the above parameters in presence of peptide, for calculating
> in absence of peptide, do i need to simulate the POPC bilayer separately?
>

I don't know how you'd infer the information otherwise, so yes, you need control 
simulations.

> I have used POPC128a bilayer from Peter Tieleman's site. I have simulations
> of POPC bilayer with peptide inserted in it for 60ns so can I simulate this
> bilayer till 60ns without peptide?
>

60 ns may or may not be enough to converge the quantities of interest.  Membrane 
simulations are often 100 ns in length or more.

> what should be the nvt, npt parameters? can I simulate in the same manner
> as Justin's KALP tutorial skipping the peptide insertion part?
>

Run settings are not a function of system composition; they are a function of 
the force field.  You don't really need to do any sort of construction at all. 
The pre-equilibrated bilayers serve as a reasonable starting point for further 
simulation.

-Justin

-- 
==================================================

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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