[gmx-users] E. coli's Inner Membrane Lipid Selection

[Jonathan Saboury]

Hello all,

I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui
to build the membrane but having difficulty deciding on membrane
constituents.

AcrB is a protein in E. coli's inner membrane: http://www.nature.com/nature/
journal/v419/n6907/images/nature01050-f5.2.jpg

Based on the below literature, I have chosen the following membrane: PYPE
70%, PYPG 14%, DPPS 8%, TYCL2 8%.

Characterization of the Escherichia coli membrane structure and function
during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC514524/pdf/1475-2859-3-9.pdf

My two main questions are:
1.) Does lipid choice affect MD simulation much? I'm using charmm36
2.) Does my lipid selection make sense? If not, why and what would you use?

Thank you for your time!! :-)