[gmx-users] simulation of a simple, solvated DPPC membrane

undergrad j gmxundergrad at gmail.com
Sat Nov 19 06:26:54 CET 2011

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:

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
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