[gmx-users] Position restrain of protein and membrane

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 15 12:48:31 CEST 2008

minnale wrote:
> Hi all,
> I embedded protein into popc bilayer by using genbox command, in 
> equilibration I want keep restrain only on protein but not on popc? can 
> I do like this or is there any manditory steps to run membrane protein 
> equibration, if it is there, Can you tell me please.
> Thank you.

Use "define = -DPOSRES" which is specified in the .top from parameterizing the 
protein under pdb2gmx.  There's nothing special (necessarily) for doing a 
membrane protein system, since all the topology information for the protein 
generally comes before the lipid/solvent stuff, anyway.


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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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