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<pre>Dear gmx-users,<br><br>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.<br>Thanks,<br><br><br>----------------<br>Message: 4<br>Date: Wed, 5 Mar 2008 23:04:22 -0500<br>From: "Justin A. Lemkul" <jalemkul@vt.edu><br>Subject: Re: [gmx-users] lateral diffusion coefficient of bilayer<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Message-ID: <1204776262.47cf6d46cf02e@webmail.vt.edu><br>Content-Type: text/plain; charset=ISO-8859-1<br> <br> <br>Did you follow the thread I started here:<br> <br><a href="http://www.gromacs.org/pipermail/gmx-users/2008-January/031797.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2008-January/031797.html</a><br> <br>I got some great information when I was getting some strange values for D. What<br>group are you using to calculate D? The suggestion that David gave me about<br>using P atoms only for the calculation led me to much more reasonable results.<br> <br>-Justin<br> <br>Quoting LeeHwan-kyu <hklee910@hotmail.com>:<br> <br>><br>> Dear gmx-users,<br>><br>> I have some questions about calculation of lateral diffusion coefficient for<br>> bilayer. I've searched this forum, but I still have problems.<br>><br>> 1) I'm trying to get lateral diffusion coefficient of the lipid bilayer , and<br>> I typed "g_msd -f ***.xtc -s ***.tpr -o msd.xvg -b 30000 -e 40000 -beginfit<br>> 1000 -endfit 7000 -lateral z". I got too high D value (which is shown as D[<br>> xxx] 0.5412 (+/- 0.0021) 1e-5 cm^2/s. I calculated it for each monolayer,<br>> and also for bilayer, but had similar values. This big value comes from the<br>> size effect ? Is there anyway to get a reasonable lateral D?<br>><br>> 2) When I ran the bilayer simulation, did I have to remove center of mass for<br>> each monolayer? My input script is jut like below. Do I need to write<br>> commends for center of mass removal for each monolayer, and run simulations<br>> again?<br>> -------<br>> nstcomm = 1<br>> comm-grps =<br>> -------<br>><br>> Thank you for your help in advance.<br>><br>> best,</pre><br /><hr />최소한의 공간에서 최대한의 정보 제공, live.com에 검색 결과 저장 기능 등으로 무장한 Live Search! <a href='http://search.live.com' target='_new'>간편하고 정확한 나만의 맞춤 검색, Live Search!</a></body>
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