[gmx-users] InflateGRO and trimer simulation

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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