[gmx-users] Molecule removal by g_membed

[Bin Liu]

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