[gmx-users] starting a peptide bilayer simulation run

[Mark Abraham]

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 
> 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?

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.

Mark