[gmx-users] InflateGRO and trimer simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 10 13:50:25 CET 2010

On 1/10/10 5:17 AM, KM wrote:
> 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

I've built multimeric systems with InflateGRO, but with a lot less constraints 
than you have :)  You can, for instance, run an inflation step with a very 
minimal scaling factor (like 1.01 or 1.05) and a very small cutoff (7 or so, but 
you'd have to play around with this) so you essentially delete lipids in place 
without moving them too much.  I don't know if the necessary lipids between the 
monomers will be affected.

As for preserving water molecules, you could probably just extract their 
coordinates from a suitably-oriented starting structure and paste them into the 
InflateGRO output.

None of this requires modifying InflateGRO, but will likely require a lot of 
trial and error, if it even works, given the very specific nature of what you need.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list