[gmx-users] InflateGRO and trimer simulation

[chris.neale at utoronto.ca]

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