[gmx-users] Re: lateral diffusion coefficient of bilayer

LeeHwan-kyu hklee910 at hotmail.com
Thu Mar 6 14:25:02 CET 2008

Dear gmx-users,

Thanks for the answer, but I already saw about P atom and tried it, but didn't work.  It looks like the problem is more related to center of mass removal or PBC (size effect).  Could you please explain how to solve this problem? Details are explained below in my previous email.

Message: 4
Date: Wed,  5 Mar 2008 23:04:22 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] lateral diffusion coefficient of bilayer
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1204776262.47cf6d46cf02e at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1
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,
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