The MARTINI forcefield for residue-based coarse-grain models allows simulation of several tens of atoms as only several large coarse-grained particles [49,50,52]. In the MARTINI model, each protein residue is represented by a backbone bead and usually one or more sidechain beads.
When preparing MARTINI simulations it is important to include only those dihedrals specified by the forcefield. Using the ``auto dihedrals'' or ``regenerate dihedrals'' feature of psfgen will create dihedrals for all possible sets of four bonded atoms. This is incorrect for MARTINI and will result in energy jumps because the dihedral potential function is degenerate for the angles of 180 degrees allowed by cosine-based angles.
When using MARTINI the following configuration parameters should be set as indicated:
cosAngles on martiniSwitching on dielectric 15.0 PME off