MARTINI Residue-Based Coarse-Grain Forcefield

The MARTINI forcefield for residue-based coarse-grain models allows simulation of several tens of atoms as only several large coarse-grained particles [63,64,69]. 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

• cosAngles $<$ enable the MARTINI cosine-based angle potential function $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not the MARTINI forcefield is being used, specifically cosine-based angle potential function. The cosine-based potential will only be used for angles in CHARMM parameter files that specify the cos keyword.

• martiniSwitching $<$ enable the MARTINI Lennard-Jones switching function? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not the MARTINI forcefield is being used, specifically the Lennard-Jones switching function.

• martiniDielAllow $<$ Allow dielectrics != 15.0 for use with MARTINI $>$
  Acceptable Values: on or off
  Description: off Allows user to specify a dielectric not equal to 15.0, ie a non-standard dielectric for MARTINI.