[gmx-users] lateral diffusion coefficient of bilayer

[Justin A. Lemkul]

Did you follow the thread I started here:

http://www.gromacs.org/pipermail/gmx-users/2008-January/031797.html

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.

-Justin

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.
>
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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