[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin Lemkul]

On 7/27/12 8:50 AM, J Peterson wrote:
> Hi Justin, Thanks for that information.
>
> I also would like to confirm with you that should I combine my metal ion too
> while I combine Protein and POPC into Protein_POPC group to be used in COMM
> removal? So that I will have a group Protein_HEM_POPC.
>

With layered systems, the COM removal groups are best set to whatever makes 
physical sense - whatever is an integral part of a layer is a viable group.  So 
I would think that any prosthetic group or ligand bound within a protein is a 
valid member of that layer.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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