Hello there! I am an undergraduate working on my thesis, which involves the simulation of a DPPC membrane. My college is small and the department does not have experience with MD simulations, so I am 100% on my own. I have successfully modeled simple proteins in water- but I want to move onto bilayers.
I am attempting to simulate a simple, homogeneous DPPC bilayer. I have a .pdb file of the membrane, along with .itp files provided by http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I am following this procedure for setting up the membrane: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html However, I feel like I am missing something? The procedure is telling me to alter a .top file to accommodate the altered force field .itp's (ffG53a6 to include Berger lipid parameters-which I have already accomplished)- maybe the .top in question is the topology of the protein that is being implanted in the membrane? I do not want a membrane bound protein in this simulation- so how do I generate a .top for a simple membrane? Is it through pdb2gmx? Do I have to manually program the system topology? Maybe someone can point me to a detailed procedure for setting up a simple membrane system from start to finish...? I am probably going to be bugging this group a lot in the next few weeks- thank you for reading this.... (Sorry if this question is confusing/sounds silly- again, I'm working on my own)
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