[gmx-users] Re: InflateGRO and trimer simulation (KM)

[mwolf at gwdg.de]

> Hello Gromacs Users,
>
> I would like to run a simulation of a trimer in a DPPC membrane. I
> really like the elegant solution that inflategro script offers,
> however I'm afraid I won't be able to use it, because I need to have
> lipids in a small space between the monomers right in the center of
> the box and these will certainly get deleted during the whole
> procedure. I also need to keep the waters that come with the structure
> of the protein.
> Do you have any idea how I can elegantly embed my trimer in a
> membrane, possibly using somehow modified inflategro?
>
> Christopher
>
We developed a new gromacs tool, g_membed, to insert a protein into a
bilayer. It works  different than inflategro. Instead of inflating and
deflating the bilayer in this approach the protein is slowly grown from a
narrowed protein to its full size during a short md run.

The paper describing this tool has just been accepted by J. Comp. Chem. As
soon as we have a doi we will merge it to the git version. For now you can
download a version from our website and compile it yourself:
http://wwwuser.gwdg.de/~ggroenh/membed.html

With this tool you can also keep the crystal waters (or for that matter
anything from the crystal structure you want to keep). If you need three
proteins in the bilayer you can insert them one at the time.
For a more elaborate manual type g_membed -h.

Cheers


-- 
Dr. Maarten G. Wolf
Max-Planck-Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11
37077 Goettingen
Germany
Phone: (+49) (551) 201 - 2320
Fax: (+49) (551) 201 - 2302
Email: mwolf at gwdg.de