[gmx-users] Coupling groups in protein-ligand-lipid simulation

Justin A. Lemkul jalemkul at vt.edu
Wed May 16 12:29:00 CEST 2012

On 5/16/12 1:01 AM, Anirban wrote:
> Hi ALL,
> I am simulating a membrane protein docked with a ligand and embedded in a lipid
> bilayer. For COM removal I am using two groups, "Prt_Lig_Lipid" and "SOL_CL".
> For temperature and pressure couplings should I use these two groups or should I
> use three groups, "Protein", "Lipid" and "Lig_SOL_CL"?
> Any suggestion is welcome.

If the ligand is bound to the protein, I would couple the protein and ligand as 
a single group.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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