[gmx-users] simulation of a simple, solvated DPPC membrane
Justin A. Lemkul
jalemkul at vt.edu
Sat Nov 19 06:29:58 CET 2011
undergrad j wrote:
> 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...?
A suitable topology for a DPPC-only system is provided as part of my tutorial:
It's rather simple and does not require pdb2gmx, just the extended 53a6 force
field. If you've already got that, you're just about done.
> 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)
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users