[gmx-users] lipid tail order
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
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
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