[gmx-users] lateral diffusion coefficient of bilayer

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 6 05:04:22 CET 2008

Did you follow the thread I started here:


I got some great information when I was getting some strange values for D.  What
group are you using to calculate D?  The suggestion that David gave me about
using P atoms only for the calculation led me to much more reasonable results.


Quoting LeeHwan-kyu <hklee910 at hotmail.com>:

> 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.
> best,
> Hwankyu.
> _________________________________________________________________
> MSN ¸Þ½ÅÀúÀÇ Â÷¼¼´ë ¹öÀü, Windows Live Messenger!
> http://windowslive.msn.co.kr/wlm/messenger/


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list