[gmx-users] integration protein-bilayer in CG

[Francesco Pietra]

Hi:

I am looking for indications how to insert a large trimer CG protein
into one of the pre-equilibrated bilayers (preferably POPC, if it
exists) of the MARTINI web site. And surround the whole with a layer
of water, if possible. I have already prepared the .itp file for the
trimer, that is, if I did correctly, the CG knows the secondary
structure of the trimer..

New to both GROMACS and MARTINI, I have experience how to that job
all-atoms with AMBER. There, a cavity into the hydrated bilayer is
first created, shaped on the protein to host.

For the moment I am at GROMACS 3.3 on a parallel machine.

Thanks for help

francesco pietra