[gmx-users] Re: Bilayer
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 8 22:00:51 CEST 2010
Please keep all Gromacs-related correspondence on the gmx-users list. I cannot
serve as a private tutor, and I do get numerous requests. You stand a much
better chance of reaching someone with useful advice by posting to the list. I
have a few ideas (see below), so I am CC'ing the list to benefit the community
and perhaps stimulate further responses. Archiving your questions and responses
will help others down the road who have the same issues. That also reduces my
personal inbox traffic :)
Clark, Tiffany D wrote:
> Hello Mr. Lemkul,
> I am a graduate student at East Carolina University and I am trying to
> construct a heterogeneous lipid bilayer for use in a md simulation using
> GROMACS. As I have been searching for help online you have emerged as
> an expert in the field with your ablity to provide the most insight and
> helpful advice. I am hoping you are willing to share some of your
> knowledge with me.
> I am trying to create a 4:1 mixture of POPC and POPG respectively. I
> will be using the Berger lipids force field (lipid parameters by D.
> Peter Tieleman). I am thinking the best approach maybe to construct a
> set of lipids (DPOPC, LPOPC, DPOPG and LPOPG) and then propagate that
There is no need to re-construct any lipids. Just extract a single lipid
molecule from the pre-equilibrated bilayers at Tieleman's site. Don't
differentiate between different stereoisomers of POPC; the topology provided by
Tieleman does not pertain to both possible forms.
> using GROMACS editconf. I am struggling with how to get things
A combination of editconf and genconf would be useful. You could construct a
small box with the appropriate lipid ratio, then replicate it with genbox -nbox
to create a monolayer of sufficient size. Create a duplicate monolayer and
rotate it with editconf, concatenate the structures, and presto, you have a
bilayer. This structure will of course require substantial equilibration (tens
to hundreds of ns) due to its artificial regularity.
> started. I have .itp files for both POPC and POPG (from
> http://moose.bio.ucalgary.ca/index.php?page=Downloads) but how do I
> generate topologies for the new positions of the lipids? I have noticed
Topologies and positions are independent. The only requirement is that the
[molecules] section of your .top matches the order of the molecules present in
your coordinate file (aside from the obvious nomenclature of atoms).
> that may people have just changed the head group and made small changes
> to the topology file
> Is the only way to create a GROMACS .top file for a lipid to write it
> yourself? What is the best way to generated the starting coordinates of
It should be very straightforward to write the topology, just #include the
necessary topologies (all of which you already have) within the .top file.
> my lipids? I have constructed each of the lipids and minimized the
> structures (using Amber), though I don’t think this will be useful for
> the construction of the bilayer (in GROMACS). The .pdb files available
Probably not. The AMBER-output structures will likely be all-atom molecules
with atom naming that has no relationship to the names defined in the
Tieleman-provided topologies. See my comment above for a reasonable (and
extraordinarily easy) method for getting the coordinates of a single lipid.
> on Dr. Tieleman’s website are bilayers and not individual lipids (would
> you advise me to start with a lipid structure isolated from one of the
Indeed, yes :)
> Any advice or recommendations you are willing to share would be most
> appreciated. None of the faculty here work with GROMACS and I am
> struggling to understand how a bilayer can be constructed based upon
> topology files (.itp) or if only amendments are possible.
Then you've been assigned an unfortunate task. What you are looking to do is
fairly complicated for someone who is unfamiliar with GROMACS and without an
immediate support system you are in for a lot of archive reading and waiting
around for free help.
What you really need to get comfortable with is the fact that a topology has
nothing to do with coordinates, thus no structure can be built from a topology.
Crafty use of editconf and genconf are all you need to build the system.
> Gratefully yours,
> Tiffany D. Clark
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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