Hi,
the new inflategro with the 'doughnut mode'
(http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want.
Ciao,
Patrick
Justin A. Lemkul a écrit :
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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Dynamique des Structures et Interactions des Macromolécules Biologiques
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