I am running some CGMD simulations of a membrane protein embedded in a model of E. coli membrane (12x12 nm bilayer with different lipids), and I want to do the analysis of the membrane thickness and area per lipid (APL). For these tasks I am comparing the performance of FATSLiM, APL@Voro, GridMAT-MD and the GROMACS tool densmap. For this I have several questions:

1 - I am running densmap as *gmx densmap -f traj.xtc -s topol.tpr -n PO4_index.ndx -od densmap.dat* selecting the lipid of interest (as the PO4 bead), previously grouped in the index file. Then I plotted the *densmap.dat* file in Origin, obtaining a color coded heatmap of each lipid for the upper and lower membrane leaflet. What are the unit for this density maps? The *-unit* options are in nm-3, nm-2 or count. If I select *-unit nm-2*, does that means number of lipids per nm-2?

2 - How different is the previous approach from the APL calculated in FATSLiM, APL@Voro, GridMAT-MD?

3 - Which is the best method for the membrane thickness calculation.




Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
+49 40 42838 2845
office: Grindelallee 117, room 250c

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