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
[email protected] | (410) 706-7441
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