[gmx-users] lateral diffusion coefficient of bilayer

LeeHwan-kyu hklee910 at hotmail.com
Thu Mar 6 04:41:35 CET 2008

Dear gmx-users,

I have some questions about calculation of lateral diffusion coefficient for bilayer.  I've searched this forum, but I still have problems.

1) I'm trying to get lateral diffusion coefficient of the lipid bilayer , and I typed "g_msd -f ***.xtc -s ***.tpr -o msd.xvg -b 30000 -e 40000 -beginfit 1000 -endfit 7000 -lateral z".   I got too high D value (which is shown as D[ xxx] 0.5412 (+/- 0.0021) 1e-5 cm^2/s.   I calculated it for each monolayer, and also for bilayer, but had similar values.   This big value comes from the size effect ?   Is there anyway to get a reasonable lateral D?

2) When I ran the bilayer simulation, did I have to remove center of mass for each monolayer?  My input script is jut like below.  Do I need to write commends for center of mass removal for each monolayer, and run simulations again? 
nstcomm    =  1
comm-grps =

Thank you for your help in advance.


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