Hello users I am trying to check water transport through a membrane protein. I ran simulation for 10 ns. In first attempt I couldn't see significant transport through protein although pore was filled. I hypothesized it could be due to osmotic equilibrium. so in my next mdrun I deleted all water molecules between z coordinate 0 to 1.2 A. Unexpectedly whole set up shifted down to fill up empty spaces left by water molecule deletion. Although I got some water molecules transporting through bilayer but in opposite direction. now i am confused if its artifact or protein is solely exporter. My query is how can i set up a osmotic potential across bilayer effectively? During visual trajectory analysis by vmd, in sequential frame I observed uncertainities in position of some water molecules (even across bilayer) . Does it mean my system has crashed?
your guidance will be highly appreciated. thank you in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
