[gmx-users] RE: Insertion of protein in lipid bilayer

[Graham Smith]

> I did follow the position restraint step in my run by restricting P8
in the
> z direction. What happened was that the 2 popc layers flipped right
off the
> bat in the md so that the head groups and water from each layer were
facing
> each other while the hydrophobic tails from each layer were situated
as far
> away from each other as possible. It was really quite bizzare and
after
> getting a few chuckles from it, I'd like to find out what I did wrong.
This
> is what I did:
> 1) got the 128 popc pdb and itp from Sir Tieleman, used
>
http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar
.gz
> forcefields

I think they haven't "really" done that, you've probably got an illusion
due to periodic boundary conditions (sketch your system replicated along
z and you'll see what I mean). The simulation you've got isn't wrong but
you may want to change the coord file and repeat it so things look more
normal. See note (c) below ...


> 2) followed the how-to html to create holes using msms.
> A few questions here:
> a) should I minimize the new membrane with hole?

It won't do any harm, but it might well work without it anyway.

> b) how critical is removing all the possible lipids that may clash
with the
> protein?

Not at all. The whole idea is that it will push the remaining ones out.

> c) I simply used vmd to manually put my proteins into the membrane
lipid and
> saved the coordinate of the protein in a seperate file. Then I copied
and
> pasted the simulation box size from the membrane  pdb file to the top
of my
> protein file. Is this acceptable? What would be the most bullet-proof
> approach?


Moving files around with vmd could perhaps be the source of the apparent
"flipping" of the lipids - e.g. if it has centered something at (0,0,0);
gromacs avoids -ve coordinates and wraps them round into the next
periodic image. I generally use editconf -center [rvec] or editconf -c
to move things around, then subsequently concatenate the pdb files and
view the result to check I've got it right.


> 3) grompp and mdrun using the following parameters.
> run.mdp
---

> A few questions here too:
> a) what would typical values be for the tau_p and tau_t?

I use tau-t = 0.1 and tau-p = 1.0 with Berendsen coupling but I don't
think it's critical, especially in an unphysical simulation like this.

> 4) I havn't got to this step yet but after the hole has been generated

> successfully generated in the membrane, do I append the protein.pdb
file to
> the end of the membrane_hole.pdb file and run a normal em/md to the
system?

Yes. Well, I normally put the protein first, but the order of the
components (protein, lipid, water, ions if you have them) doesn't
matter, as long as they're the same in the pdb file and the topology. 

Graham

############################################

Dr Graham R. Smith
Biosystems Informatics Institute
Newcastle upon Tyne NE1 4EP




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