[gmx-users] lipid tail order

[Archana Sonawani-Jagtap]

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 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?

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

Please help me.......

thanks in advance
-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339