[gmx-users] starting a peptide bilayer simulation run
Mark.Abraham at anu.edu.au
Tue Apr 24 09:44:45 CEST 2007
nur avneet wrote:
> 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
> 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?
I don't know anything about makehole, but if you don't need a hole, you
surely don't need to make one :-)
> 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....
I don't know what you mean by "concatenating the two systems". Your mdp
file is probably not the problem, although you can test for this by
checking that a bilayer without solute is stable.
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