[gmx-users] lipid tail order

Archana Sonawani-Jagtap ask.archana at gmail.com
Thu Oct 17 10:57:36 CEST 2013


I want to plot
1.  -SCD (lipid tail order parameters) profile for both the chains (sn1 and

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,
Mumbai, India.

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