[gmx-users] lateral diffusion coefficient of bilayer
hklee910 at hotmail.com
Thu Mar 6 04:41:35 CET 2008
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
Thank you for your help in advance.
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