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Dear gmx-users,<br><br>I have some questions about calculation of lateral diffusion coefficient for 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 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?<br><br>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? <br>-------<br>nstcomm = 1<br>comm-grps =<br>-------<br><br>Thank you for your help in advance.<br><br>best,<br>Hwankyu.<br><br><br /><hr />강력한 폴더 공유 기능과 무료 문자 메시지, 오프라인 쪽지 보내기 기능까지! <a href='http://windowslive.msn.co.kr/wlm/messenger/' target='_new'>MSN 메신저의 차세대 버전, Windows Live Messenger! </a></body>
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