[gmx-users] starting a peptide bilayer simulation run

nur avneet nuravneet at yahoo.co.in
Tue Apr 24 09:23:43 CEST 2007

Dear all
 I want to study my peptide in a bilayer system and so for this i got the structure and topology for the lipid bilayer from the site moose.bio.ucalgary.ca
 I want to study the orientation and interactions of the peptide with the outer surface of the membrane, do gain insight about how the peptide shall start penetrating. Is it still necessary to use makehole?
 Can i start the run by placing my peptide in the outer region of the bilyer system and then concatenating the two systems and starting the simulation. I tried this method, but it leads to the disruption of the bilayer. Please guide me...n let me know the parameters of the  mdp file that i am missing....
 Thanks in advance
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