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 <[EMAIL PROTECTED]>: > > 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
