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

Justin Lemkul jalemkul at vt.edu
Mon Jul 23 13:56:57 CEST 2012

On 7/23/12 7:53 AM, J Peterson wrote:
> Thank you so much for that, Justin.
> Now I could expand the bilayer.
> I've another query. My protein has a small N-terminal portion embedded in
> the membrane, I would like to insert only this part into the membrane during
> 'packing the lipid around the protein' step in your tutorial. Initially I
> was trying to do simulation only with this TM region and then attaching the
> rest of the protein with this TM region and simulate the whole system. But
> was time-taking.
> Can you please guide me to pack the lipid bilayer only around a 33-residues
> long peptide in my protein and rest with water?

Position your protein manually using editconf -center such that it is placed 
appropriately relative to the membrane and follow the same procedure in the 



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


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