Hi All, I am simulating a system of lipopeptides embedded into a lipid bilayer. I have a question about how g_membed works.
My bilayer has three kinds of lipids. Let's call them lipid_1, lipid_2, lipid_3. Sodium ions are used to balance the charges. When I invoke g_membed, it will ask for which group to embed in the membrane. In my case, obviously it is the group Lipopeptide. Then g_membed asks for a group to embed Lipopeptide into. Should it be the joint group of lipid_1, lipid_2 and lipid_3? Or something else? I used make_ndx to generate an index group called Membrane by merging group Lipid_1, Lipid_2 and Lipid_3. It seems it works with g_membed. It gives the following information: Will remove 2 Lipid_1 molecules Will remove 1 Lipid_2 molecules Will remove 3 Lipid_3 molecules Will remove 7 SOL molecules Will remove 0 NA molecules Will remove 0 Lipopeptide molecules Apparently the behaviour of g_membed is what I want. But what concerns me is I don't know whether the removal of 0 Sodium ions is just a coincidence or it's a deterministic action by g_membed. Of course I don't want the removal of ions as it would cause a charged system. So my question is under what conditions will g_membed remove ions? Thank you in advance. Regards Bin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
