[gmx-users] CG lipid diffusion coefficient

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Fri Mar 29 13:55:38 CET 2019

Hi all,

I ran some CG simulations of a protein inserted in a lipid bilayer, with 
several lipids. I used the msd tool to compute the lipid (using the PO4) 
diffusion coefficient. For one of the lipid I got D = 0.6 x 10^-5 
cm^2/s, which is 600 um^2/s. According to the Martini website "To 
compare the diffusion coefficient obtained from a Martini simulation to 
a measured one, a conversion factor of about 4 has to be applied to 
account for the faster diffusion at the CG level due to the smoothened 
free energy landscape (note, the conversion factor can vary 
significantly depending on the molecule in question)." (J Phys Chem B. 
2009 Feb 5; 113(5): 1501–1510.)

The value I get is 2 orders of magnitude higher of a comparable value of 
6 um^2/s.

Would this make sense?



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
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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