[gmx-users] integration protein-bilayer in CG

Francesco Pietra francesco.pietra at accademialucchese.it
Mon Sep 28 19:27:53 CEST 2009


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

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