[gmx-users] Building dimer system using MARTINI

James Starlight jmsstarlight at gmail.com
Fri Mar 18 14:21:56 CET 2016

Dear Gromacs Users!

I wonder to ask suggestions regarding assembly of the oligomeric
systems parametrized using martini ff.

Briefly using only 1 type of protein the situation is very simple - 1)
prepare box for the monomer using martinize, 2) equilibrate it and 3)
make replicas vwithin one system using genconf.

however what I should to do if I dealing with the simulation of 2
different proteins ? E.g is it possible to make initial system using
martinize for 2 different proteins within one system or I should
alrernatively make 2 different systems and after equilibration join
them together? How it could be achived for the oligomeric membrane
protein system assuming that I want to start simulation for 2 unbound
receptors within 1 membrane and simulate its assosiation ?

Thanks for help!!


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