[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 29 17:41:32 CEST 2008

minnale wrote:
> HI users,
>       I have embedded protein in popc bilayer and ran the minimisation 
> succesfully , before going equilibration I would like to confirm one 
> thing that how to run the equilibration with on which system keep 
> position restrain?
> 1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
> or 2. keep position resrain on each system at a time and
>   3.is it require to keep position restrain on water?
> Could you tell me clearly pls
> Thanks alot in advance

If you "equilibrate" your system with every element of it restrained, I 
think you will accomplish absolutely nothing.  Typical procedures for 
membrane proteins involve equilibrating with restraints on the protein 
only, allowing the lipids to pack around the protein. 


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


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