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
--
========================================
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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