liang wrote: > Dear all, > I am a freshman to membrane protein simulation, and i was wondering > how to choose lipid molecules for my system. > As we know, there are lots of lipid molecules: DMPC, DPPC, POPE..... > but how do people decide that which type of lipid to use? and what > kinds of criteria should we follow? Lipids differ in their chain length, chain saturation, head groups size. There are, e.g., phospholipids, glycolipids. Some are ionic, zwitter-ionic, or neutral. They differ in the phases they adopt at whatever temperature, there are wedge-like and cone-like shapted lipids, etc. There are parameters for some lipids available (including those you mentioned), and for many there is no topology availabe (yet). Membranes may include glycerin, ...
I guess you need to think abount the quetion you want to address and then choose the lipid you want to simulate. An important issue is, or course, to simulate a lipid membrane which you may compare to experiments. Cheers, Jochen > Thanks so much! > Liang > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 -- ************************************************ Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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