[gmx-users] MARTINI simulation of protein-protein recognition

[James Starlight]

Dear Gromacs users!

I am looking for some tutorial for the MARTINI simulation of
protein-protein recognition dealing with the big membrane protein
simulated within the membrane and its assosiation with the small water
soluble protein. The question - is it possible in existing Martini
system conisdted of only membrane protein solvated in membrane with
water to
i) increase box size on Z
ii)add some water
iii) put another water soluble protein in new space (on the distance
of the initial membrane protein complex)
iv) edit topology of new system and run new md

assuming that i,ii and iv are trivial the problem here is the iii step :-)

or alternatively if I would like to run new simulation with those 2
proteins (in the unbound form) how I can prepare such complex system
consisted of big protein in membrane plus water soluble protein
unbound from it?

Thanks!

Gleb