[gmx-users] Molecule removal by g_membed
jalemkul at vt.edu
Thu Aug 15 23:44:26 CEST 2013
On 8/15/13 3:05 PM, Bin Liu wrote:
> 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?
Whenever you delete molecules from a system, there will have to be corresponding
changes in the topology, some that may require you to re-calculate the number of
ions you need. Molecules are deleted simply based on physical overlap. Full
details are in the g_membed paper (dx.doi.org/10.1002/jcc.21507).
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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