Hello,

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.

Thanks

Best

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to