Try the doughnut mode in the newest version of the program -- it's
meant for exactly this situation.
http://www.csb.bit.uni-bonn.de/inflategro.html
-- original message --
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
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